Can anyone point me towards a method to merge gam files that are created by using ' vg map ' to map illumina reads to my genome graph?
I would like to be able to map all of...Can anyone point me towards a method to merge gam files that are created by using ' vg map ' to map illumina reads to my genome graph?
I would like to be able to map all of the...sequencing runs separately and then merge…
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I'm new to the bioinformatics space, and I'm attempting to merge one dataset with the 1000 Genomes dataset (as the reference).
However, I'm unsure on how to do this. I've researched a bit, and...I'm new to the bioinformatics space, and I'm attempting to merge one dataset with the 1000 Genomes dataset (as the reference).
However, I'm unsure on how to do this. I've researched a bit, and some peop…
Hi everyone,
I have two cytoscape interaction networks I am merging (v3.9.0 on Mac). My goal is to see which nodes are unique to one particular network, knowing that many nodes are found...Hi everyone,
I have two cytoscape interaction networks I am merging (v3.9.0 on Mac). My goal is to see which nodes are unique to one particular network, knowing that many nodes are found in...both networks. I…
If I want to merge a largish (>1000) number of VCF files, I find that it is useful to follow a hierarchical strategy: split the initial set...of VCF files into many smaller sets of VCF files, merge each of these smaller sets *in parallel* (using `bcftools merge`), and then merge the resulting intermediate merged VCFs...files is very large.)
What makes this strategy effective is the possib…
updated 9 months ago • kynnjo
Hello all,
I am new to this whole realm of PLINK and SNP Arrays.
I have got 3 plink datasets all .ped, .map, and .fam files. I want to merge them to do a population genetic diversity analysis.
One dataset is Goat 70K SNP array by Illumina. The remaining two are...realm of PLINK and SNP Arrays.
I have got 3 plink datasets all .ped, .map, and .fam files. I want to merge them to do a population gen…
updated 18 months ago • Umer
I have a more general question. I do targeted, paired-end DNA resequencing. Before the alignment I merge overlapping read paires, which improves my variant outcome in that way, that I have much less artefacts or pseudogenvariants...I'm happy with it.
But it seems that most people doesn't merge overlapping read pairs. I couldn't find any good reason for that. In the most posts I have read about t…
updated 12 months ago • finswimmer
To preparing larger Dataset for velvet, I merged two unmapped human reads files and now I have 3 questions ?!
1) Is this the right way to increase the quality of velvet output...To preparing larger Dataset for velvet, I merged two unmapped human reads files and now I have 3 questions ?!
1) Is this the right way to increase the quality of velvet output (I mean length of contig which I produced) …
updated 12.1 years ago • khikho
Hi everyone,
I have individual vcf files of indels and want to merge them into a big one, but only extract chromosome 3,4,5,7,8 into a unified file. The list of vcf files is in `round1_indel.txt...What I did is:
bcftools merge -l round1_indel.txt -o round1_indel.vcf -r 3,4,5,7,8
However, the output is only for chromosome 3. The document file for bcftools
HiSeq data. I have processed the data and at a point where i have flow cell A and B runlevel data merged. Can anyone tell me the command/tool which i can use to merge flowcell A bam to flow cell B bam. My bams are indexed and sorted
I search rs80314515 ([https://www.ncbi.nlm.nih.gov/snp/?term=rs80314515][1])
rs80314515 has merged into rs10204648
I wonder if there is a data base about which SNPs are merged? (For all the SNPs currently known)
And another
I have a two fasta files, file 1 and file 2 ,they have a lot of overlapped sequences but not all of them, here I want to merge these two files into
updated 5.5 years ago • horsedog
for a particular R-package or commands to read, write, concatenate and relabel the sequences in a fasta formatted file. I know other GUI softwares but I need to perform this in R.
Please help me.
Regards
Awan
Hi all,
I'm trying to merge some rather large VCF files using the joinx1.8 vcf-merge tool. The problem is that before the merging has finished, I receive...a segmentation fault error. It seems that > 90% of the input files are successfully merged before the error occurs. I've repeated the command using joinx1.6 and 1.7, but they too produce a segmentation fault...installing the prerequ…
updated 8.4 years ago • jonorman
I asked a form of this question previously here http://biostar.stackexchange.com/questions/3676/merging-genomic-segments-separated-by-some-distance-number-of-markers but did not get much response.
Given genomic regions...I asked a form of this question previously here http://biostar.stackexchange.com/questions/3676/merging-genomic-segments-separated-by-some-distance-number-of-markers but did not…
two independent chipseq for a transcription factor with two replicate in each experiment. I want to merge the bam file of replicates but I do not know what condition is required for merging bam file. Every replicate file has...depth and their alignment is also not similar. What is exact condition when bam files can be merged? Any leads would be appreciated
I have 3 vcf files containing 10, 15 and 20 different individuals in each file. The merging command "bcftools merge -0 --missing-to-ref", was used to merge the vcf files together. After merging, in a location of the...merged vcf file, the genotype (GT) is changing to 0/3; whereas in the unmerged vcf file, the same GT was 0/2. In addition, variant-specific...parameters (e.g. SOR, QUAL, BaseQRankSu…
updated 3.6 years ago • Apurba
Hi,
I have six data sets from different platforms, I annotated probs in each data to gene symbole. I want to merge them like so I have six data sets with the same gene symbols in rows. I used intertection but data sets returned NA. how to...six data sets from different platforms, I annotated probs in each data to gene symbole. I want to merge them like so I have six data sets with the same gene …
updated 7.1 years ago • A
Hi, I have a weird question. But I'm looking for a software which not just merge the paired reads but also writes them in a new file.
When a software matches a pair of reads it writes them in the output...fastq (or fasta), but you don't have the option of knowing what they paired. I've checked some of them but mostly they create a file with the...SAMPLE_JOINED.fastq
the first two files would co…
updated 5.2 years ago • oscar.nvergara
Hello.
I want to merge 7 Seurat objects and do batch correction. How can I do this?
I'm going to use the merge() function to merge seurat objects. If
updated 23 days ago • sooni
I have about one thousand vcf files, and this is a ridiculous amount to type by hand into vcf-merge. Is there a way to merge all of these files without typing each name?
I tried putting all of the files into a text file and...using stdin, but vcf-merge doesn't support this,
i.e.
vcf-merge < list.txt > merge.vcf
Maybe this problem stems from creating this many vcf files
Good afternoon,
I meet a question to merge my objects by using scanpy.
As you can see in the following figure, each objects has obs * var values. But after I merge them...adata has 0 vars.
The code I used is:
```py
adatas=[sk1, sk2, sk3, b7]
adatas=ad.concat(adatas, merge='same')
```
I am wondering how to solve the problem. Thanks.
![enter image description here][1]
[1]: /media/image…
updated 10 months ago • Andy
I am merging tons of indel VCF files using vcf-merge. It does not work and I found these VCF files cannot pass the vcf-validation. Is...I am merging tons of indel VCF files using vcf-merge. It does not work and I found these VCF files cannot pass the vcf-validation. Is there any way to merge indel VCF files? Thanks!
#CHROM POS ID REF ALT
1 62297 . T TCTTC
1 769138 …
path/to/outputfolder/ /path/to/input/*.sorted.dedup.bam
output=$2
mkdir $output
merged=$(basename ${output})
echo $merged
#samlist=$(printf 'I="%s" ' "$@")
samlist=$(printf '%s ' $@)
echo ${samlist}
cat << EOF |cat #qsub
#!/bin/bash -l
#PBS -N rna...qut.edu.au
##PBS -m bea
cd \$PBS_O_WORKDIR
conda act…
Is it possible to merge two indexes created using BWA version 0.7.17 (https://github.com/lh3/bwa)? I need to create many BWA index files that included...genomes are different from run to run.
I've come across several different programs that can merge BWT index files, such as https://github.com/holtjma/msbwt, https://github.com/jltsiren/bwt-merge, and https://github.com/felipelouza...output file…
updated 5.6 years ago • rgc255
I would like to generate the VCF file with the genotyping calls of all chromosomes but I need to merge the BIM files first. I generated a file "mergelist.txt" with the names of the bim files to merge and I tried the command below...plink --bed name1 --fam name2 --merge-list mergelist.txt --make-bed --out merged
or:
plink --bed name1 --fam name2 --merge-list mergelist.txt --make-just-bim…
updated 2.1 years ago • mgdrnl
I merged two datasets in plink1.9. It worked, but I did get the error "multiple positions seen for variant" and "variants have the...same position". How do I resolve this when trying to merge the datasets again?
And, I tried to merge two eigenstrat format files using mergeit -p. However the new merged dataset was
updated 7 months ago • Jd
Hello,
I am trying to merge specific regions of bigWig files into a single bigWig file. I know about `bigWigMerge`, which does the merge part, but how...can I merge specific regions of bigWig files?
Ideally I'd like it to be in a single step, but would it be necessary to do it in many steps...e.g. extract region of file 1, extract region of file 2, merge extracted regions)
Thank you
updated 6.6 years ago • romgrk.cc
STAR on fastq files, got sam and OutSJ.out.tab files as its output.
Now for 2 pass mapping i want to merge all the out.tab files. How can i merge all these files?
Thanks
updated 6.3 years ago • bisht20diksha
i have been trying to merge some ped/map files. i had removed or renamed the duplicated in the map file so i no longer get a duplication warning.
/home...i have been trying to merge some ped/map files. i had removed or renamed the duplicated in the map file so i no longer get a duplication warning.
/home/chrystalla/plink-1.07-x86_64/plink --bfile snp_exc_1 --merge snp_exc_2.map snp_exc_2.ped -…
updated 7.3 years ago • stalo_92
breed X, so they are biological replicates. I have also another 6 files from breed Y.
I have merged them using BCFtools merge
bcftools merge -Oz L10A2_SNP.vcf.gz L10A_SNP.vcf.gz L10B_SNP.vcf.gz L10C_SNP.vcf.gz...RossC_SNP.vcf.gz: 426710
RossD_SNP.vcf.gz: 271401
RossE_SNP.vcf.gz: 306445
and for the merged file
bcftools view -v snps merged_Ross_SNP.vcf.gz | grep -v -c '^#'
T…
updated 16 months ago • mohsamir2016
I have several fasta files of assemblies from different samples. Is there a recommended method for merging de-novo assemblies? I have 88 assemblies
updated 5.6 years ago • O.rka
to differentially expressed genes across different samples. But now I have problem extracting fasta sequence for some differentially expressed genes.
I had a gtf file from augustus which I tried to merge it to gtf files...gene name like g123, g6352, ect, but I have IDs like CUFF 2.1, CUFF 12.1, etc.
I already extracted fasta sequence from the genes having appropriate gene names. However I don't…
hello.
Is there a place where I can download merged rs number information as a file?
I want to know the rs number before merging and the rs number after merging.
You can search
chr1 320 400 region4 +
chr1 330 410 region5 +
I am using bedtools merge to merge sequences that overlap - however, I really need to set a minimum overlap cut-off. Bedtools merge will overlap bookended...to change this.
E.g. regions 1 and 2 overlap by only 20bp, and in this case I would not like them merged. However, regions 4 and 5 mostly overlap, and I would li…
I have ten MSAs per gene for a group of organisms, that I need to merge (e.g. 10x cytB, 10x COI...). How can I dealign these MSAs for realignment together? Alternatively, is there a way to "merge" multiple
updated 17 months ago • jbt38
Hi,
I want to merge 2 networks but I want different color of their node. For example N1's vertices should be represented with color "Red" while...of N2's with color "Green". So that I can identify which nodes in the merged network belongs to which network (N1 or N2).
I am using following code:
```r
library(igraph)
dd <- read.table("g1.txt")
g1 <- graph.data.frame...g2, "color", …
bcftools view --exclude-types indels,mnps,bnd,other example.vcf -o example_1.vcf
Then I want to merge gvcf files using bcftools:
bcftools merge --file-list sample.txt -g ref.fa -O v -o merge.vcf
But it is not working. I am getting...an error like `Failed to merge alleles`. I am not sure if I am using correct commands. Thank you so much for your help and time
updated 4.6 years ago • evelyn
Hello!
Right now I am having trouble with merging multiple bed, bim, fam files.
Here is my code:
```
$ ./plink.exe --bfile 1data --merge-list merge.txt --dog --make-bed --out merged
Options...in effect:
--bfile 1data
--dog
--make-bed
--merge-list merge.txt
--out merged
16221 MB RAM detected; reserving 8110 MB for main workspace.
Warning: Multiple positions seen...with 3+ alleles pre…
IDs but share the same Gene Symbol, which I'm storing as an attribute in another column.
How can I merge nodes based on the value they have in the Gene Symbol attribute/column, while keeping all the edges of the original nodes...I tried playing with Tools --> Merge --> Network but I can't get it to work (i.e.: nodes do not merge).
Any help is appreciated!
Thanks
Hi! I have two input files, `fastas.txt` with multiple FASTA sequences, such as shown in an example below:
>Blap_contig79
MSTDVDAKTRSKERASIAAFYVGRNIFVTGGTGFLGKVLIEKLLRSCPDVGEIFILMRPKAGLSIDDRLKKMLELPLFDRLRKERPSNLKK...additional_header_information.txt` with strings, such as:
XYZ
aksjdkasdj
And I' like to merge the strings from the second file with the headers in the first…
expressed genes in each of the tissues separately. My question is which of these samples should I be merging with cuffmerge? I can either merge all four samples to create the one .gtf, or merge just the samples from the same tissue
Hello All,
I'm trying to merge 2 vcf.gz files and I'm running into a strange behavior using bcftools merge. All of the positions in my second file are...being setting to missing (./.) during the merge. Does anyone have any tips for how I might fix this problem?
Here is my command:
```bcftools merge -O v -m file1.vcf.gz file2.vcf.gz
I had 3 replicated bam files, and I merged them. I wanted to see if there is a way to reverse this (going from the merged to original bam files
the SNP calling of whole-genome sequencing for a non-model organism and I have a doubt regarding the merging of the paired-end data. When should it occur? I already did all the pipeline (quality filtering, mapping, sorting, remove...duplicates, and SNP calling with GATK), but in GATK best practises I never saw anything about merging the paired-end files. Could you light me on this?
Thanks,
Gabri…
Hi,
Before mapping , we have to merge PE reads?If yes, what's the way? Or doing map separably
updated 7.6 years ago • Arash
Hi there I'm facing the task of merging the CRAM files for 25 human samples.
Each on is divided into 12-13 CRAM files (total of 322 individual CRAMs), for which...m aware `samtools` can do so; however, I have limited experience with CRAM files let alone having to merge a large number of them. So, my question is what is the exact command I should use *e.g*
samtools merge --input-fmt-option C…
Hello. I have numerous bam files which I need to merge into a single bam file. How do I know whether I need to first index and sort the bam files
I am using Dindel for calling Indels from exome deta. Can anyone do a favor by telling how to merge foo.libraries.txt.I did, cat on them, but it did not work.Emits Lib. error at 3rd stage
updated 10.5 years ago • Rajendra Bahadur Shahi
I am merging multiple single-sample VCF files into one multi-sample VCF file with bcftools merge using this command:
bcftools...merge --info-rules NS:sum -o outFilePath dir/*.gz
Previously, using bcftools 1.1, the output VCF file contained one row per position
I've been thinking a lot about this problem and I don't know how to solve it.
I have a fasta file with microRNAs precursors and a bed file with the coordinates of this precursors in a genome.
fasta file microRNAs...LQNS02278089.1 848490 848552 LQNS02278089.1_34110 882643.1 - 848490 848552 0,0,255
I also have a fasta file of mature microRNAs sequences that I would like to map to the precursors…
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