Biostar

8,824 results • Page 1 of 177

ENSSASP00005000004"; protein_version "1"; I have a reference genome : sequence.fasta and a bam file : ILS_W_V_558_S2_R1_001_val.bam that looks like this : samtools view ILS_W_V_558_S2_R1_001_val.bam | head NB551648...i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:36 YS:i:0 YT:Z:DP I want to see gene specific coverage from the bam file. result should look like gene_name in 1st col…

linux WGS Bioinformatics SARS CoV2

updated 3 hours ago • Adyasha

However, to do this, WGS/WES data is required, which we don't have access to (we can't handle the BAM files due to memory issues). I considered using bcftools consensus to generate FASTA files from the VCFs, but HLA typing...software requires reads (FASTQ or BAM files), and I haven't found a way to obtain those types of files from VCFs. Then, I learned about HLA imputation, but it also requires

formats vcf fastaq HLA_imputation HLA_typing

updated 2 days ago • Javier

score recalibration. This is followed by a second round of SNP calling using the recalibrated bam files. However, I am now analyzing SNPs in a sister species to the focal species that has the annotated reference genome

SNPs GATK BQSR RNA-seq

updated 3 days ago • dtnondorf

amp; trimmed Illumina fastq (paired end) to ref genome using bowtie. 2. Convert SAM file to sorted BAM file using samtools. 3. Use MACS2 to call peaks. This was done on Galaxy and I used all standard parameters except for changing

MACS2 DiffBind ChIP-seq

updated 3 days ago • yvonneh

Hi, I was aligning short reads to a customized gfa file using vg giraffe. I tried to extract mapped reads from the gam files, first using vg surject to convert the gam file to a bam file. However, I had this error "No reference-sense paths available in the graph; falling back to generic paths." I tried to add...to extract mapped reads from the gam files, first using vg surject to convert th…

updated 3 days ago • Hang

for mitochondria variant discovery using mutect2. I am currently trying to Align the unmapped BAM file with the reference aligned BAM and shifted reference aligned BAM using the MergeBamAlignment command. I keep getting

mutect2 mitochondria

updated 4 days ago • ernestine.kubi

OSError: truncated file and the only out put i get is a .bam file and no .tsv. Please help-- Thank you! </module

Telescope RNA-seq

updated 5 days ago • eleven11

NCBI. I have successfully mapped the raw reads to the reference genome and obtained the results in a BAM file. However, when I try to run the FeatureCounts tool on the BAM file using the GTF file, I am unable to find any variability

featureCounts

updated 6 days ago • Ravita

the options and if Mutect behaves the same in both cases below. In the first below I provide 3 bams with 3 different ids in each and I specify the 2 ids as normal. In the second only the --tumor-sample is provided. Exclamation...normal-sample !{third_sample_id} \ --max-reads-per-alignment-start 90000 \ --bam-output "result/!{tumor_sample_id}${PREFIX_FOR_OUTPUT}${part_prefix}.reali…

cancer mutect variant-calling GATK somatic-variants

updated 6 days ago • Alexandros

the product of multiple FAST5 being concatenated perhaps incorrectly. Others in the past have used `.bam` files produced from this data and it contained millions of reads, as expected. For my analysis, I cannot use those `.bam` files

metagenome base-calling fastq nanopore

updated 7 days ago • Gio

Dear Biostar Community, Currently I'm doing a phylogenetic study on 37 samples. The samples were sequenced using MIG-seq. The sequencing data is in fastq format. Using Julien Catchen's Stacks, I was able to create a SNP matrix. From the SNP matrix, I was able to do a PCA and find that there are three tightly grouped clusters. Additionally, the tree built by RAXML has three major clades all wi…

population-genetics phylogenetic

updated 9 days ago • SineWave

to assign these haplotigs to chromosomes. After mapping haplotigs to chm13 with minimap2, I have a bam file with aligned haplotigs. I want to create a fastq from this bam file that contains the aligned haplotig reads as well

Assembly phased Haplotype Annotation

updated 10 days ago • turcoa1

A Coverage \ --dbsnp dbsnp.vcf` I would like to ask why they may require the bam file for this function? I know that the mandatory field input.vcf already computed from the bam file itself. What may affect...if I do not include the bam file? Best, [1]: https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator

gatk VariantAnnotator

updated 11 days ago • QX

Hi Everyone, I analyzed 200 datasets from NCBI using the same code. However, when I applied the analysis to my original dataset, I noticed that the outputs were incorrect. After discussing with my supervisor, he conducted the same analysis using his own code, and it produced the correct results. I thought maybe my code was wrong, so I tried using his code, but the results were still incorrect. I…

fpkm Counts Rsubread rna-seq

updated 11 days ago • sehriban.buyukkilic

I am using bat (rhinolophus sinicus) snRNA-seq brain samples located [here][1]. The associated paper is located [here][2]. The samples were prepped with the MGI DNBelab C4 scRNA Preparation Kit and were sequenced on the BGI DNBSEQTM technology platform. I downloaded all the bat brain tissue samples with parallel-fastq-dump. Below is an example of downloading a single sample. parallel-fastq-…

STARSolo scRNA-seq STAR snRNA-seq MGI

updated 12 days ago • atowns21

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

Hi, I am looking at a rare splicing event, and would like to keep only reads in a specific interval that have an alignment at that location. With a simple `samtools view alignment.cram chr1:12345-12456` I also get all reads that are spliced across that interval (screenshot below). How do I get rid of reads that do not actually align at this location? Bonus points if I can still keep the m…

samtools bam splicing

updated 13 days ago • WouterDeCoster

ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False</module

Ciriquant

updated 14 days ago • Atul K.

aDNA), specifically two high coverage samples of Neanderthal and Denisova. The latter has on single BAM file aligned to GRCh37 and already sorted; unfortunately, Neanderthal has five BAMs which were not sorted and needed to...one post I thought to re-head the five files with the following: ``` samtools view -H nea_<#>.bam | grep -v "^@RG" | samtools reheader - nea_<#&gt…

samtools bam

updated 15 days ago • Matteo Ungaro

Hi, I am currently preprocessing my fastq files to make analysis ready BAMs. I received cram files from the centre, for which I have done following steps so far. 1. Cram2fastq 2. Split fastq (as they were...Hi, I am currently preprocessing my fastq files to make analysis ready BAMs. I received cram files from the centre, for which I have done following steps so far. 1. Cram2fastq …

Deduplication UMI

updated 15 days ago • Lipika

rate. Now how can I find about the gene through reads data. Is there any way to find through sam or bam file that which chromosomal position are maximum reads aligning to? Thanks

crisper-edited alignment match

updated 16 days ago • analyst

10-19_Data/13_Refs/13.03_Geno/reference.fa BAMLIST=/home/my_user/my_account/10-19_Data/16_Lists/bam-final-list.txt OUTDIR=/home/my_user/my_account/10-19_Data/14_Out-data/14.03_SNP-calls N_IND=`cat /home/my_user/my_account...10-19_Data/16_Lists/bam-final-list.txt | wc -l` angsd \ -bam $BAMLIST \ -ref $REF \ -out $OUTDIR/minMapQ20minQ20_minInd145.25_setMinDepthInd2_setMinDepth150setMaxDepth600

lcwgs ngsTools ANGSD genomics

updated 17 days ago • DanielEB_fisk

Hi all, Looking for resources for free software/packages that accept fastq files (or bam) as input and return a '23 and me-like' output. Either health- or ancestry-oriented, the only criteria are free, comprehensive

SNPs genomics NGS VCF

updated 17 days ago • joe

Hello, I need to add CB tags to my bam files. Below is what I'm doing. I see the tags when I pipe to stdout but the tag is not written to the new bam. What is it that I'm missing...Thanks! ``` # $LINE is the path to the original input bam, there is one bam for each $cell samtools view -h -b -o ${cell}.bam ${LINE} | sed -e "/^@/! s/$/ CB:Z:${cell}/" # or samtools view -h -b ${LINE} | sed -e "…

samtools bam

updated 17 days ago • Maria

genome for the same bacteria I found off NCBI (the fasta file ends in .ffn) I converted the sam to bam, sorted, and indexed bam file using sam tools. I know I need to use something like bedtools to quantify the bam file, but I am

differential-expression transcriptome

updated 17 days ago • siddharth.patel.153

Hello, I am currently using Longshot for variant calling on my BAM file. However, I'm encountering an issue where the number of variants generated does not match the expected count. Could...path/to/output_directory/output_filename.vcf" # Run Longshot with specified parameters longshot \ --bam "$bam_path" \ --ref "$ref_genome" \ --out "$output_vcf" \ --min_cov 1 \ --min_mapq 1 \ --mi…

long-reads variant-calling ONT minion longshot

updated 17 days ago • samuelkalandarov2002

Dear all, I was wondering if anyone came across a tool that would correctly extract reads from `all_contigs.bam` file generated by 10x VDJ pipeline? Official `bamtofastq` does not support these files, but they are often the only thing that is available from GEO/SRA. Thank you in advance, -- Alex

TCR VDJ BCR 10x

updated 18 days ago • predeus

I have that fungal sequenced by PacBio and result in three types of sequences 1. CCS sequencing (bam and fastq file) 2. CLR sequencing (only have bam file) 3. CLR_CCS sequencing (only have bam file): followed CCS sequencing using...may play a role like the. reference genome when doing the alignment. Since I only have the bam file for #2 and #3, can I transfer the bam file to fastq and then do…

assembly

updated 18 days ago • ycts

4 -q --very-fast -x mm9/mm9 {input} | samtools view -Sbh -o {output) {log} Sort with Samtools: (a BAM File) samtools sort {input} -o {output} MACS2 Peak Calling: macs2 callpeak -t {input} -n {output} -f BAM -g mm -B -q 0.01 Everything ran successfully

ChIP-Seq batch-effect sequencing

updated 18 days ago • dmj6ab

Hi everyone, I'm working on a clustering analysis of multiple samples. I have BAM files that went through QC. My current workflow involves: 1. Variant calling with bcftools (To replicate GVCF behavior...Hi everyone, I'm working on a clustering analysis of multiple samples. I have BAM files that went through QC. My current workflow involves: 1. Variant calling with bcftools (To replicate GVC…

vcf bam bcf snps

updated 18 days ago • George

Hi, I tried to transfer cram file to bam file using: ``` samtools view -T ./hg38new/hg38.fa -b -o 12bj1_withrefernece_bam.bam GTEx_Analysis_2021-02-11_v9_WGS_CRAM_files_GTEX

sequence samtools bcftools

updated 19 days ago • me

Nanopore, do I need to remove duplicates after using minimap2 ? or i should keep them ? (the bam files generated using minimap2 are used by freebayes in order to detect variants

duplicates ONT minimap2

updated 19 days ago • quentinperriere

DEXseq (for differential exon usage) and Slueth (differential gene expression) analysis on some TCGA BAM files. As the BAM files can be from different centers and created in different sequencing batches I was looking to control

Batch-effect RNA-Seq Differential-Expression

updated 19 days ago • vakul.mohanty

an error "Value was put into Pairinfo Map more than once" while running picard's MarkDuplicates on a bam file that was created by merging files from three different runs. I found several threads on Biostars addressing this...lanes, or presumably any other identifier). Is this something that can be performed on the three bam files that I generated before merging (perhaps with an appropriate …

picard MarkDuplicates

updated 20 days ago • shpak.max

I want to perform SV calling on nanopore data. From the resulting bam file after aligning and sorting I add the MD flag with samtools calmd and then run sniffles sniffles -m alignment_md.bam

SV sniffles StructuralVariant

updated 21 days ago • njornet

vcf path/output_vcf_file --ploidy 2 --min-alternate-fraction 0.05** It's worth noting that my BAM files were generated using Minimap2. I'm curious if there's a method to enhance FreeBayes' capability for variant detection

reads freebayes long

updated 21 days ago • quentinperriere

is used but with this what I need to generate .vcf or .g.vcf file? And for somatic mutation which bam I need to use llike tumor, normal or blood. For germline do I need to generate vcf or gvcf for each 3 samples

germline variants somatic

updated 22 days ago • anitharavichandran2211

Hi everyone, I'm utilizing the GATK Best Practices for analyzing mitochondrial NGS data. I utilized FastqToSam to generate a ualign BAM file. Following that, I aligned the fastq with BWA MEM. Per the Best Practices, I executed MergeBamAlignment with the ualign BAM and aligned BAM. I observed that the original BWA MEM BAM's read1 and read2 counts differ from those after MergeBamAlignment. BWA ME…

MergeBamAlignment samtools flagstat

updated 23 days ago • ThomasLam

SAMPLES = config["samples"] # target rule rule all: input: expand("mapped/{sample}.bam", sample=SAMPLES.keys()) # STAR mapping rule star_map: input: reads = lambda wildcards: (SAMPLES[wildcards.sample]['r1'], SAMPLES...wildcards.sample]['r2']) output: "mapped/{sample}.bam" params: index = "$HOME/1-rna_editing/ref/STAR_genome_index", …

snakemake

updated 24 days ago • yixinzeng

Hi all, After I generate BAM or SAM files from my data, and have the coordinates of the 5' end of each read, how can I get the 3bp sequence on either side of

SAM genomics sequencing

updated 24 days ago • nrav58

load a reference gene model (i.e. a GTF/GFF3) - load short read and long read RNAseq tracks (i.e. BAM/CRAM files) - via drag and drop of the RNAseq reads, create or modify gene structure. Store the created/modified gene structures

structure gene

updated 25 days ago • William

I downloaded bam "slices" from a database (TCGA), which correspond to a subset of the entire alignment, corresponding to a small set of genes

variant calling

updated 25 days ago • ramiro.barrantes

to a specific coverage /depth but requires fastq input and I would prefer to downsample my BAM files so I don't have to re-run my alignment on many samples again

nanopore BAM QC ONT downsampling

updated 26 days ago • eesiribloom

were aligned to Ensembl's genome, the `##contig` headers of the PON/gnomAD do not match the input BAM files (GATK errors out, related to reference and feature contigs not matching). I've been looking if there are any Ensembl

GATK Mutect2 ensembl

updated 27 days ago • DGTool

Hi Biostars community, I need help to create .bam file from .sam. I used the code: `samtools view -bS x.sam > x.bam`, and error report is: ``` [E::sam_hdr_create] Invalid header line...Hi Biostars community, I need help to create .bam file from .sam. I used the code: `samtools view -bS x.sam > x.bam`, and error report is: ``` [E::sam_hdr_create] Invalid header line: must

RNA-Seq

updated 27 days ago • demekemewa13

**Hello everyone**, I’ve been trying to perform RNA velocity analysis, and I’ve been having a few issues with my results. I was hoping someone with more experience could help me out maybe! Basically I’m just trying to generate a figure to show through a non biased way a trajectory analysis showing the transition of stem cells into a subtype of cells. The issue is that after doing my…

RNAvelocity

updated 28 days ago • phhelou5

all_genomes.fsa ./$GENOME_DIR/$INDEX_BASE 2 - Using HISAT2 to align and convert the sam to bam HISAT2_INDEX=$ReferenceFolder"/yeast_index" OUTPUT_DIR="./Reads" READ1=$1 READ2=$2 # Align reads to the combined genome hisat2...alignment_summary.txt \ | samtools view -b -o $OUTPUT_DIR/alignment.bam - #convert stdout to bam file The reports suggest the …

HISAT2 BWA Alignment

updated 4 weeks ago • theworldsagainstme

Hello, I am trying to input multiple bam files as input for Lima (multiple runs) but I don't see anywhere in the documentation on whether this is even feasible. Has

Long-read-sequencing PacBio

updated 4 weeks ago • aa9gj

experience. Cramino is a faster replacement for [NanoStat][2], and extracts features from cram and bam files that are useful for quality assessment of long read sequencing data, including read lengths and read identities

long-read nanopore pacbio

updated 4 weeks ago • WouterDeCoster

samtools mpileup but it taking too long, how long does it usually take to generate a bcf file? My bam file is 26.9 gb, and the sorted bam file is 17.6 gb

Bam samtools sam alignment

updated 4 weeks ago • K

8,824 results • Page 1 of 177

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Meme-Tools: Bit score

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DEXSeq multiple time points

How to find the most frequent alternative-splicing event from DEXSEQ data?

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