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Forum: Bioinformatics 10-22-2012, 04:54 AM
Replies: 0
Views: 832
Posted By AdrianJ217
CIGAR Format and DEGSEQ

Hi Everyone. I'm having difficulty interpreting CIGAR output from SSAHA2. Could anyone please help me interpret the following CIGAR output?:

cigar::50 ERR023002.2 31 17 - Tb927_11_03_v4 233403...
Forum: Bioinformatics 10-15-2012, 04:58 AM
Replies: 7
Views: 1,612
Posted By AdrianJ217
Rahul, thanks so much but it only gave me 3 that...

Rahul, thanks so much but it only gave me 3 that lined up. I checked and the problem is that the one liner you gave me only looks for those lines that exactly match up and gives me those results,...
Forum: Bioinformatics 10-15-2012, 04:15 AM
Replies: 7
Views: 1,612
Posted By AdrianJ217
I mean where column1 (Gene_Horn) and column3...

I mean where column1 (Gene_Horn) and column3 (Gene_DEGSeq) are the same, print a column containing the genes that overlap (called column1), along with column2(Uninduced_Horn) which is the reads of...
Forum: Bioinformatics 10-15-2012, 03:09 AM
Replies: 7
Views: 1,612
Posted By AdrianJ217
Hi, thank you. Here are the first several lines...

Hi, thank you. Here are the first several lines of the file:

Gene_Horn Uninduced_Horn Gene_DEGSeq Uninduced_DEGSeq
Tb04.24M18.150 12 Tb04.24M18.150 172
Tb04.3I12.100 21 Tb04.3I12.100 11...
Forum: Bioinformatics 10-15-2012, 12:40 AM
Replies: 7
Views: 1,612
Posted By AdrianJ217
Perl Script

Hi, I have 2 sets of 2 columns of data. One set has a column of gene names and the other column is the number of reads per gene. The second set of columns includes one column also with gene names...
Forum: Bioinformatics 09-02-2012, 01:48 AM
Replies: 9
Views: 2,395
Posted By AdrianJ217
dpryan, if you could send me a copy of that I'd...

dpryan, if you could send me a copy of that I'd really appreciate it. My email is:
aajavaherian@gmail.com

Thank you so much!
Forum: Bioinformatics 08-31-2012, 04:37 AM
Replies: 9
Views: 2,395
Posted By AdrianJ217
dpryan, thank you so much. Just one more...

dpryan, thank you so much. Just one more question. You said to copy the 2nd column of one to the empty 3rd column of the other, but why wouldnt I copy both columns of one to the other, to have 4...
Forum: Bioinformatics 08-30-2012, 11:24 AM
Replies: 9
Views: 2,395
Posted By AdrianJ217
Thank you

Great, thank you so much, and then can you tell me what commands I need to type into R in order to run it using my file?
Forum: Bioinformatics 08-30-2012, 07:27 AM
Replies: 9
Views: 2,395
Posted By AdrianJ217
DE Seq

Hi, I am new to using DE Seq. I have 2 files, output from htseq, containing the name of the genes with the # of reads next to them. One file has reads before induction of rna interference...
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