User: 2nelly

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2nelly220
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Geneva,Switzerland
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Posts by 2nelly

<prev • 135 results • page 1 of 14 • next >
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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 17 days ago by 2nelly220
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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 17 days ago by 2nelly220
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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 11 weeks ago by 2nelly220
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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 11 weeks ago by 2nelly220
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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 12 weeks ago by 2nelly220
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Comment: C: How to put CutAdapt in path for running TrimGalore?
... gedit ~/.bashrc Then do what genomax suggests ...
written 3 months ago by 2nelly220
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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 3 months ago by 2nelly220
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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 3 months ago by 2nelly220
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snpeff disable intragenic
... Hi all, Does someone know how to disable intragenic flag in snpeff annotation like for upstream downstream splice exon etc? I know that there is a description about intragenic variant in snpeff website. However, I noticed that these variants are falling in intergenic, intronic or utr regions of no ...
annotation snp sequencing written 5 months ago by 2nelly220
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Comment: A: Chip-seeker heatmap around the peak centers
... hi Jingyue, In your example you plot the profile of ChIP peaks binding to TSS region (distance of peaks from TSS). What is exactly the other plot, you are talking about? Using the center of the peak as reference and plot the signal of bam or bigwig file? p.s. sorry editors, I accidentally ...
written 14 months ago by 2nelly220

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