User: 2nelly

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2nelly210
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Geneva,Switzerland
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Posts by 2nelly

<prev • 133 results • page 1 of 14 • next >
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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 1 day ago by 2nelly210
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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 1 day ago by 2nelly210
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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 9 days ago by 2nelly210
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Comment: C: How to put CutAdapt in path for running TrimGalore?
... gedit ~/.bashrc Then do what genomax suggests ...
written 16 days ago by 2nelly210
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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 16 days ago by 2nelly210
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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 17 days ago by 2nelly210
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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 10 weeks ago by 2nelly210
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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 12 months ago by 2nelly210
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Comment: C: finding specific SNPs in VCF files
... that s fine, you can use it as it is ...
written 12 months ago by 2nelly210
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Answer: A: Find similar values in two gene lists
... You can try this awk 'NR==FNR {end[$1]; next} ($1 in end)' list1 list2 In case you want to match different columns change the first $1 with the number of column you want to compare or the second $1 to match with another column ...
written 12 months ago by 2nelly210

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