User: Afagh

gravatar for Afagh
Afagh20
Reputation:
20
Status:
New User
Location:
United states
Last seen:
2 months ago
Joined:
8 months, 3 weeks ago
Email:
f************@gmail.com

Posts by Afagh

<prev • 13 results • page 1 of 2 • next >
4
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5 follow
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(Closed) Problem with using "until" in "bash script"
... I don't understand why it doesn't print 0 : z=0 until (($z < 1)) do echo $z done I don't understand why it prints 2 (2 is not less than 1) : output: **z=2** **until (($z < 1))** do echo $z done **output:2** ...
bash written 4 months ago by Afagh20
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Comment: C: Parsing gff files using python and awk
... Thanks, what if I want to extract the gene name? I tried $F[8]=~/Name:(\c+)/ didn't work. ...
written 4 months ago by Afagh20
6
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Parsing gff files using python and awk
... I have two text file that have lines like this: NC_013520.1 RefSeq gene 2229 3341 . + . ID=gene1;Name=Vpar_0002;Dbxref=GeneID:**8635442**;gbkey=Gene;locus_tag=Vpar_0002 I want to extract gene ids of all genes, and then compare it with another file that I have. I wrote this script but it doesn't c ...
awk written 4 months ago by Afagh20 • updated 4 months ago by WouterDeCoster20k
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Comment: C: Number of genes
... Yes, I do. Should I use them? I thought I need to use mapping results! ...
written 6 months ago by Afagh20
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Comment: C: Number of genes
... Hi, A transcription unit is the sequence between sites of initiation and termination by RNA polymerase; may include more than one gene ...
written 6 months ago by Afagh20
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Number of genes
... I need to find the number of genes in a transcription unit based on the mapping results. I don't know how to get this information. I have the start and end site of each transcription unit and also strand. Can I use SAM or BAM file to extract the number of genes in each TU? How? ...
rna-seq written 6 months ago by Afagh20
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Comment: C: finding overlapping genes
... Thank you :) I modified it to this code, and it worked :) awk -F '[, \t]' 'BEGIN { n = 1; }{ for (**i = 2**; i <= NF; i++) { if ($i in ht) { print "non-unique element "$i" was found on "ht[$i]" and **"$1"** "; for (j in f) { if (f[j] == $i) f[j] = 0; } } else { ht[$i] = $1 ; f[n] = $i; n++; ...
written 8 months ago by Afagh20
3
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finding overlapping genes
... I need a list of lines that do not have any overlap, and a list of lines that have overlap. We can have any number of genes in each line (separated by comma)! I like to do it in awk, but I'm not very familiar with all the commands. L1 ycjM,ycjN,ycjO,ycjP,ycjQ,ycjR,ycjS,ycjT,ycjU,ycjV,ymjB L2 ...
overlap awk written 8 months ago by Afagh20 • updated 8 months ago by Alex Reynolds20k
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Comment: C: Best tool for finding Boundary Pairs
... Thank you! So, I don't need to use the start site or -100 base and things like that? Okay, I'll write the script in python! ...
written 8 months ago by Afagh20
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Comment: C: Best tool for finding Boundary Pairs
... @Macspider Yes, you are right :) ...
written 8 months ago by Afagh20

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