User: 2nelly

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2nelly230
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Posts by 2nelly

<prev • 137 results • page 1 of 14 • next >
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Comment: C: Copy number variations from WES data
... I mostly use VarScan for this job. it is pretty straight forward and designed specifically for exome sequencing. http://varscan.sourceforge.net/copy-number-calling.html ...
written 5 days ago by 2nelly230
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Answer: A: Is there anyway to get a unix parallel command to write to standard output
... Why don't you try xargs? find *.bcf | sed "s/.bcf//g" | xargs -n1 -P10 -I{} sh -c "bcftools stats {}.bcf | grep 'number of records:' | cut -f 4 > {}.txt" -- {} -P stands for the number of parallel processes you want to run. I don't know what are exactly the names of your files, so excuse a ...
written 3 months ago by 2nelly230
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Comment: C: Bizarre CIGAR string
... Let s say that this is a task they gave me to do as a test. I know the potential solutions like convert back to fastq and realign. However, I suspect that this is a kind of pitfall they set me up on purpose. I just want to know what can cause this strange attitude apart from modifying the file on pu ...
written 4 months ago by 2nelly230
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Bizarre CIGAR string
... Hi all, I was given a bam file to process for variant calling. However GATK gives CIGAR error. Checking the respective aligned reads I noticed a very strange possible error. Do you have any idea what can cause this misconception with the CIGAR string after alignment with bowtie? A00129:298:H7 ...
alignment next-gen sequencing written 4 months ago by 2nelly230
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Comment: C: Nest 2 for loops in a single command line
... yes, but only for printing the name files. Caro-ca generalized the example. In fact, he wants to apply a conversion from bed to vcf. Thence, he will replace echo with something else. Of course he can use find command and then xargs to do the same thing. But maybe it is better for him to have one s ...
written 6 months ago by 2nelly230
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Answer: A: Nest 2 for loops in a single command line
... What about this: for i in /home/caroca/strains/SRR*; do for f in $i/results/*nonredundant.bed; do echo $f; done; done also you can have the same result in one loop: for f in /home/caroca/strains/SRR*/results/*nonredundant.bed; do echo $f; done; ...
written 6 months ago by 2nelly230
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Answer: A: TSS metaprofile using Deeptools
... If you can upload the first lines of your test.gtf, we can help you. Alternatively, you can try to convert gtf to bed format. For me the bed format below works like a charm: chr1 2985742 3355185 PRDM16 369443 + chr1 6845384 7829766 CAMTA1 984382 + chr1 8412464 8877699 RERE 465235 - ...
written 7 months ago by 2nelly230
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Comment: C: How to put CutAdapt in path for running TrimGalore?
... gedit ~/.bashrc Then do what genomax suggests ...
written 7 months ago by 2nelly230
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Answer: A: annotationPeaks.pl algorithm for defining promoter-Tss
... According to homer documentation: > The process of annotating peaks/regions is divided into two primary > parts. The first determines the distance to the nearest TSS and > assigns the peak to that gene. The second determines the genomic > annotation of the region occupied by the cente ...
written 7 months ago by 2nelly230
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Answer: A: Understanding the output from HTseq-count
... This looks like the alignment file. Are you sure that having a look at HTseq output? Normally, you should get a two column file (gene name or ID and counts per gene). ...
written 7 months ago by 2nelly230

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