User: Afagh
Afagh • 20
- 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
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4
votes
0
answers
159
views
5 follow
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answers
... 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** ...
written 4 months ago by
Afagh • 20
0
votes
2
answers
246
views
2
answers
... Thanks, what if I want to extract the gene name? I tried $F[8]=~/Name:(\c+)/ didn't work. ...
written 4 months ago by
Afagh • 20
6
votes
2
answers
246
views
2
answers
... I have two text file that have lines like this:
NC_013520.1 RefSeq gene 2229 3341 . + . ID=gene1;Name=Vpar_0002;Dbxref=GeneID:**8635442**;gbkey=Gene;locus_tag=Vpar_0002
I want to extract gene ids of all genes, and then compare it with another file that I have. I wrote this script but it doesn't c ...
written 4 months ago by
Afagh • 20
• updated
4 months ago by
WouterDeCoster ♦ 20k
0
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0
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286
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Comment:
C: Number of genes
... Yes, I do. Should I use them? I thought I need to use mapping results! ...
written 6 months ago by
Afagh • 20
1
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0
answers
286
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0
answers
Comment:
C: Number of genes
... Hi,
A transcription unit is the sequence between sites of initiation and termination by RNA polymerase; may include more than one gene ...
written 6 months ago by
Afagh • 20
5
votes
0
answers
286
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0
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... I need to find the number of genes in a transcription unit based on the mapping results. I don't know how to get this information. I have the start and end site of each transcription unit and also strand. Can I use SAM or BAM file to extract the number of genes in each TU? How? ...
written 6 months ago by
Afagh • 20
0
votes
1
answer
336
views
1
answers
Comment:
C: finding overlapping genes
... Thank you :)
I modified it to this code, and it worked :)
awk -F '[, \t]' 'BEGIN { n = 1; }{ for (**i = 2**; i <= NF; i++) { if ($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
Afagh • 20
3
votes
1
answer
336
views
1
answer
... 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 ...
written 8 months ago by
Afagh • 20
• updated
8 months ago by
Alex Reynolds ♦ 20k
0
votes
2
answers
410
views
2
answers
... 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
Afagh • 20
0
votes
2
answers
410
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2
answers
... @Macspider Yes, you are right :) ...
written 8 months ago by
Afagh • 20
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