Biostar

8,824 results • Page 2 of 177

varScan.variants.filter* I get the following output: 27841 variants 27841 failed to get readcounts for variant allele 0 had read position < 0.1 0 had strandedness < 0.01 0 had var_count < 4 0 had var_freq < 0.05...lt; 0.2 0 passed the strand filter Apparently, the problem is with obtaining the readcounts. The bam-readcounts files were …

VarScan2 fpfilter.pl

updated 3.0 years ago • vanessagpds

each base" I ended up with the following options: (1) samtools mpileup / bcftool call (2) bam-readcount (3) igvtools (4) pysamstats The performance of the `IGVtools` is same as the `Pysamstats`, and I liked the output (it is...clear and that's exactly what I need). I understand that probably the `bam-readcount` use another default options, therefore results are different…

samtools bam-readcounts igvtools pysamstats

updated 6.6 years ago • IrK

Hi, I recently ran bam-readcount on my bamfile and I noticed something weird about my result chr1 201334382 G 58077 =:0:0.00:0.00:0.00:0:0:0.00:0.00

bam-readcount

updated 7.1 years ago • Apoorva

Hello, I'm trying to install bam-readcount and it keeps failing during the make step. I'm on MacOS Monterey with the M1 chip (if that makes a difference). I used...any thoughts about how to fix this? The installation is: git clone https://github.com/genome/bam-readcount cd bam-readcount mkdir build cd build cmake .. make This is the error it shows: […

bam-readcount

updated 2.0 years ago • erin.brettmann

Hi All I’m using bam-readcount on a bam file with ~60000 alignments (stitched reads which span the 374 bp length of the amplicon reference). bam...readcount -w -1 -q 0 -b 0 -f my_ref.fa sort.bam > bam_readcount.q0b0_w-1 2> bam_readcount.error Here is a “head” of the output: my_ref

bam-readcount error warning alignment bam

updated 7.5 years ago • mark.rose

how to count mismatchs number at each position in BAM file ? I found BAM-readcound, but it seems that the bug isn't solved yet : [https://github.com/genome/bam-readcount/issues/19][1] any...alternative method ? [1]: https://github.com/genome/bam-readcount/issues/19

alignment

updated 6.8 years ago • Chadi Saad

To build bam-readcount, I cloned the bam-readcount repository, made a separate build directory, and from it entered `cmake `, resulting...Configuring incomplete, errors occurred! See also "/local/scratch/PACKAGES/src/bam-readcount/14Apr2016/build_directory/CMakeFiles/CMakeOutput.log". See also "/local/scratch/PACKAGES/src/bam-readcount

build error

updated 7.4 years ago • twtoal

use as ground truth to compare which tool behaves better at counting the number of reads within a BAM file for instance. So far, I've ran `bcftools mpileup` which is supposedly only a wrapper for `samtools mpileup` (which I also...ran) and a third tool called `bam-readcount` (https://github.com/genome/bam-readcount). I ran all three tools on the same data set making sure that the quality...the a…

genome alignment read counts ground truth

updated 3.2 years ago • Marius

Hey! I'm running bam-headcount to get allele frequency from mapped reads. I got the following error messages: Minimum mapping quality is set...0 [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). Segmentation fault: 11 My bam file was created with samtools view -hbS sample1.sam &gt...sample1…

bam-readreadcount bam bam_header_read

updated 7.2 years ago • fangqiong.ling

whether these variants are being mistakenly filtered in some samples. I could just plug each bam file into IGV or USCSC but I'd rather have an approach that uses the source bam files and just calculates an allele frequency...frequency (bcftools) or operate on a restricted set of sites (glactools). I've settled on using [bam-readcount][2] and parsing the output files. Can you suggest alternative…

sequencing

updated 4.5 years ago • kevin.stachelek

Hi all, I am running bam-readcount program on one of my bam files of size 7Gb on a machine with 24G memory. I provided 2.5M positions and reference

bam-readcount multi threading slow speed

updated 8.1 years ago • fizer

Hi, I'm trying to install bam-readcount. Following the git installation instructions I get stuck in the 'make' step. Here is the somewhat long error message

installation

updated 10.2 years ago • Karol Pal jr.

is that my subject is polyploid. I already checked that there are two bases on that posistion using bam file, IGV and bam-readcount. What I want to know is base group(?). ex) A..........G (A,G) C..........C (C,C) or A..........C (A,C) C..........G (C,G) If base group of reference is (A,G) and base...similar work of haplotype phasing. Of course I'm not sure. I can't check information like …

bam sam genotype

updated 2.7 years ago • gh

bam-readcount -f /v2/reference/human_g1k_v37_decoy.fasta -l test.bed /pValSeq/run202/20180430-0002.bam -q 20 -i -d 1000 returns...Minimum mapping quality is set to 20 Expect library: KapD-20180607-0002 in BAM Floating point exception (core dumped) Any ideas?? Tried all other options etc BAM file from novoalign, exome, reference and...bam otherwise ok $ bam-readcount -v bam…

next-gen sequencing

updated 5.8 years ago • p2.leo

I am trying to install bam-readcount in a centralized location for our cluster, which means downloading "source" and building in a non-standard location

bam-readcount

updated 22 months ago • sally.boyd

Hi! I'm trying to get the allele count for some snps in my bam files. The variant calling was done by haplotypeCaller. The allele count in the output doesn't represent the real number...of reads I have in my bam file, whitch is what I want. I tried with bcftools mpileup, but the output only shows genotype liklyhoods. Also tried bam-readcount

SNP alignment sequence

updated 5.8 years ago • le.marcorin

I'm trying to convert my bam files to count data with the help of feature counts in command line, I used the code: featurecounts -T 8 -a /Users/ria/Desktop...bowtie_2/GCF_000001405.39_GRCh38.p13_genomic.gtf -g 'transcrip_id' -o readcounts/readcount1.txt bam files/-.bam (readcounts is a the directory for dumping the output) the error I'm getting is: ERROR...temporary directory is no…

featurecounts rna-seq

updated 23 months ago • gina02

Hi. I want to use bam_readcount pipeline. So I visit https://github.com/genome/bam-readcount and I downloaded the source files. First I ran `git clone https://github.com/genome/bam-readcount.git` to download...pc, and then I tried to compile bam_readcount command. that is shown below. ``` cmake /path/to/bam-readcount/repo make deps make ``` But when I run `cmake /path/to/bam-readcount/repo`,…

sequencing software-error

updated 2.4 years ago • mangfu100

Biostars masters knowledge I was wondering if raw read count tables such as: ``` chr start end readcount chrX 16635 83737 9999 ``` can be converted to bam file formatting. I know that bam files can be used to obtain read counts

alignment bam

updated 2.1 years ago • Sakti

I mapped pair end reads to CDS transcripts using BWA. If I do sorting of bam fine by not using -n flag than its worting: For sorting: /home/yog/software/samtools-1.3.1/samtools sort 216_5W_Ca1.bam...I mapped pair end reads to CDS transcripts using BWA. If I do sorting of bam fine by not using -n flag than its worting: For sorting: /home/yog/software/samtools-1.3.1/samtools sort 216_5W_Ca1.b…

RNA-Seq

updated 7.4 years ago • Bioinfonext

The manual says "Before proceeding you will need to obtain and compile bam-readcount (https://github.com/genome/bam-readcount). You will also need to generate a samtools pileup (not mpileup) indel ﬁle...I wonder how could I get a indel pileup file? just simply use samtools to convert normal/tumor bam? samtools pileup -f $reference $normal_bam Thanks!Wei

somaticsniper next-gen

updated 2.5 years ago • heartheone

calling. As a result of `VarScan2`, I have six VCF files that must be processed individually and `bam-readcount` tool is a part of this processing. The use of bam-readcount depend on the type of variant; if I have somatic variant...calls I should use tumor BAM file as bam-readcount's input and reference BAM for germline and LOH variants correspondingly. It is possible to do three...file on the b…

snakemake if-else python

updated 4.5 years ago • Jokhe

of reads supporting each allele (i.e. A=1, T=0, C=1, G=200, N=0) at each desired position of a bam with PE data (paired-end NGS data). The most similar tool which I have found for this task is [bam-readcount][1] which basically...to avoid merging overlapping reads before counting if possible [1]: https://github.com/genome/bam-readcount

bam-readcount overlapping-reads PE data

updated 3.3 years ago • pau.rodriguez.sodupe

to prevent this error without success. I found that bam_readcount fails for the 3 of the biggest bam (3, 5, 6): [jflucier@ip29-mp2 vl_samples]$ ll -h *.bam -rw-rw-r-- 1 jflucier jacques 55M Jul 26 09:54 1.90.mka.bam -rw-rw-r-- 1 jflucier jacques...6.90.mka.bam Here are the command I am running: [jflucier@ip29-mp2 vl_samples]$ ./programs/bam-readcount/bin/bam-readcount -f vl_r…

software error

updated 5.8 years ago • jflucier

Hi, I ran bam-readcount to get coverage per nucleotide. I got the result after getting this warning ` > “WARNING: In read DHDC08P1_0264...2494:140080#CTTGTA: Couldn't > find single-end mapping quality. Check to see if the SM tag is in BAM” This was the command: bam-readcount -f ../index/hg38.fa -q 1 -b 20 -l all.Germline.hc.var normal.sorted.bam > all.Germline.hc.readc…

bam-readcount varscan fpfilter snp calling

updated 5.4 years ago • Rahil

Can edgeR take normalized readcount table directly (I want to use other functions of edgeR but I prefer to normalize the data myself) Thank you! The question

updated 7.4 years ago • muhe1985

Installing bam-readcount / bam-readout I've already installed the dependencies and I've been googling for solutions: sudo yum groupinstall

bam-readcount bam-readout make c++config.h

updated 7.1 years ago • jnowacki

Hi everyone, I am new to Bioperl so please bear with me. I have a bam file and a chr-position file that looks like this: ``` 10 1156771 10 37484026 10 78483209 10 82960189 ``` I have to calculate the...Hi everyone, I am new to Bioperl so please bear with me. I have a bam file and a chr-position file that looks like this: ``` 10 1156771 10 37484026 10 78483209 10 829…

pileup perl bioperl

updated 2.5 years ago • Sameer Chavan

of elevated mutations. Previously, I've used bwa to align reads and used my sorted and indexed bam file as input to the program bam-readcount (https://github.com/genome/bam-readcount) to count the frequency of mutation at

dCas9-deaminase off-target SNPS WGS dCas9

updated 15 months ago • pd378

that it will not work with newer versions. To process files for the perl scripts, I tried to get bam-readcount installed with that version of samtools, but ran into errors (not with cmake, but with definitions). I don't remember...the error exactly, but it wasn't with sam.h or cmake, etc. I ended up installing samtools 0.16 and bam-readcount installed fine. My question is, how do these two pr…

samtools

updated 10.7 years ago • DoubleD

I download `TCGA-BLCA` HTSeq readcounts file and find some samples have 2 files. Like: $grep TCGA-BL-A0C8-01A gdc_sample_sheet.2019-09-10.tsv f832dfd0...I download `TCGA-BLCA` HTSeq readcounts file and find some samples have 2 files. Like: $grep TCGA-BL-A0C8-01A gdc_sample_sheet.2019-09-10.tsv f832dfd0-f52e

TCGA

updated 4.6 years ago • MatthewP

Hi, After aligning my rna sequences, and getting bam files, I used bam-readcount in this link [bam-readcount][1] to get the total read counts per position and sample. My data is paired...description here][4] I am skeptical if I am doing anything wrong? [1]: https://github.com/genome/bam-readcount [2]: https://rdrr.io/bioc/DESeq2/man/fpkm.html [3]: /media/images/e4888276-d295-4cf2-8f8f-2…

Read FPKM Normalize count RNA-Sequnce

updated 20 months ago • Nemo

Hi folks, I used this option to downsample the bam files. Am I doing it correctly? samtools view -s 0.15 -b input.bam > input_15X.bam Then I used this input_15X.bam to generate...wig file using HMMcopy. readCounter -b input_15X.bam > input_15X.wig Building index for input_15X.bam, please hold Index creation successful

BAM downsample depth wig

updated 6.1 years ago • bioinforesearchquestions

each sample has a median value less than 1) Below is my code[2]. rz2rpkm <- function(expr) { readcount <- expr # expr is a matrix of mean per-base read coverage with gene in rows and sample in columns readcount <- readcount...6:ncol(readcount)] read.length <- 75 exoniclength <- expr[,"ExonicLength"] for(j in colnames(expr…

mean per-base read coverage

updated 9.3 years ago • lin.pei26

Is it possible to convert bam to bam? I have bam produced by default BWA; but I may also need bam filtered by tossing out those with mapping quality< 20...We can convert sam to bam with a quality cut-off as 20, but storage of sam file is painful (simply too large). So just wondering if I can convert default...bam to quality-control bam, so that I only need to store bam file in my system. …

bwa bam samtools

updated 12.4 years ago • Bioscientist

Hello, I am started learning Hadoop Bam. But couldn't figure out the steps how to to split the bam file. For example, I have a file called `Example.bam`. I loaded the file...into hdfs: hadoop fs -put Example.bam ./ When I tried: hadoop jar /usr/local/hadoop-bam/hadoop-bam-7.0.0-jar-with-dependencies.jar I got: ``` Command: cat concatenation of partial SAM and BAM files …

hdfs hadoop genome bam

updated 2.1 years ago • shalini.ravishankar

I would like to know, can someone post a working example of converting a BAM file to CRAM and BAM again? I tried samtools, cramtools but each time, the BAM tags get mangled. Can someone show me how to get...view file1.bam | md5sum ed071dff8d60c74eefd1d14eb1f4bb21 then convert to CRAM, back to bam file2.bam such that: samtools view file2.bam | md5sum ed071dff8d60c74eefd1d14eb1f4b…

bam cram

updated 6.8 years ago • ElUretsky

Too many parsing exceptions encountered; exiting In the end after running the supported protocol 1 (bam-readcount and fpfilter), I got 0 variants that passed the filter: printf "\nRun bam-readcount\n" bam-readcount/bin/bam-readcount

varscan

updated 7.0 years ago • cafelumiere12

I'm curious if bam_readcount is sensitive to the quality score encoding (phred+33 vs phred+64). I've run across a situation in which bam_readcount calculates the average quality score at a given position, but if you look at the actual pileup file at that position, the average quality score is very different (for example, bam_readcount calculates the average quality as 12, whereas the bamfile sho…

updated 11.2 years ago • loeblabstuff

I have used the Deeptools2 packages to produce a plot comparing profiles of histone binding relative to gene start and ends. However the first sample only reaches about 2 on the Y axis, and the second lays around 0. So I am wondering if I am using it incorrectly? In particular the use of normalisation between the merged ChIP reads that are at least 3x coverage compared to the single input samp…

deeptools

updated 3.6 years ago • Ian

I've got two bam files I want to compare, A and B, but bam B comes in a different order of chromosomes as the ones in A. What is the best tool to resort...bam B in the same order of chromosomes as the one in bam A

bam

updated 10 months ago • 14134125465346445

all, I am mapping to a transcriptome for bisulfite sequencing and would like to revert the output bam to a 'genome-mapped' bam - is anyone aware of a simple command line tool that can take a genome/gff and transcriptome-mapped...bam file and return a genome-mapped bam? Thanks

genome bisulfite bam transcriptome

updated 2.5 years ago • joe

run VarScan fpfilter for 3 .hc.vcf files (somatic, germline, LOH), however when I run this command bam-readcount -q 1 -b 20 -l all.Somatic.hc.var -f hg38.fa tumor.bam > all.Somatic.hc.readcount I get this error > [fai_load

picard NormalizeFasta varscan bam-readcount

updated 5.5 years ago • Rahil

I have just begun exploring Lincoln Stein's excellent Bio::DB::Bam perl module and have an elementary question. Is it possible to edit values of an Bio::DB::Bam::Alignment alignment object? Here...is a dead simple script that just copies a bam file. my $bam = Bio::DB::Bam->open("in.bam") ; my $fix = Bio::DB::Bam->open("out.bam", "w" ) ; my $header = $bam->header(); $fix-&…

bioperl samtools perl

updated 11.0 years ago • Owen S.

Hello Everyone, Can someone explain me on how to load a .bam file into hdfs using hadoop bam

genome bam hdfs hadoop

updated 9.1 years ago • shalini.ravishankar

Hi, I am trying to extract reads from bam file that aligned to a specific region. For this porpuse I used bam2bed and bedmap to specify position on my reference...is ok. Finally reads can be extracted to bed file. Now, I am trying to change my output (bed) to bam file using bedtobam bedToBam -i sorted.bed -g mm9.chrom.sizes > sorted.bam Everything looks fine but in the end m…

bam quasirecomb bed

updated 2.8 years ago • kperlejewski

chicken heavy and light chains and I want to do pca plot on them. I know I have to convert them to BAM file first but I don't know which tool to use - FastqtoSam or Bowtie2. One gave me unaligned BAM and another gave aligned BAM...Then, I used multiBAMsummary tool to see which file was correct but both BAM file gave me an error saying file '0.bam' does not have BAM or CRAM format. Where did I g…

bam fastq

updated 4.8 years ago • zliew

I don't know enough about genomics files. I have a human tumor sample of bam, which used bwa and sambamba aglined and targged with duplicated reads. I used the below of commands converting the bam...file to a wig file required by HMMcopy. /path/hmmcopy_utils/bin/readCounter --window 1000000 --quality 20 \ --chromosome "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y" \ /path/dat…

HMMcopy Copy-number-analysis R

updated 13 days ago • SSSJec

if anyone knows how to convert the ENCODE generated tagAlign file (combo of several replicate BAMs) into a merged BAM file? Or is it necessary to take the individual replicate bam's and merge them separately

ENCODE tagAlign bam

updated 6.5 years ago • rbronste

Hi, I was looking for a tool to convert a bam file in genomic coordinates to transcriptomic coordinates (using a GTF reference). Is there a fast way to do this for large...bam files? Such tool would filter out reads that do not map to any transcript. Let me know if you have any suggestions, Thanks, Daniel

bam samtools

updated 7 months ago • dfernan

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