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Old 08-06-2014, 07:00 AM   #12
essepf
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Location: Switzerland

Join Date: Aug 2014
Posts: 5
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Hi pm2012

Thanks for your reply.

The output files I have are on this format.

gene reads_WR1
610005C13Rik 2473
0610007N19Rik 15
0610007P14Rik 1291
0610008F07Rik 149
0610009B14Rik 0
0610009B22Rik 361
0610009D07Rik 272
0610009E02Rik 4
0610009L18Rik 8

when you say, filtered, you refers to what?

command I used to generate the count:

samtools view file.bam | htseq-count -s no -i gene_name - mus_musculus.gff > WT_results_counts.txt

Thank you for your help
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