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Old 04-23-2012, 03:35 PM   #3
Kcornelius
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Location: Los Angeles

Join Date: Apr 2012
Posts: 14
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ok, the cuttdiff part seems to run now for 2 sets, one having a gtf with only chrX chrY and chrM. The sorting with one gtf file was done according to the header file I got for cuffmerge but is not running? So what could go wrong...

Given the ensembl reference, I first substitute the chromosome IDs so that they correspond to the bowtie-index. Then I sort out each chromosome:

Code:
for i in 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7 8 9 M X Y; 
do 
grep "^chr$i[[:blank:]]" Homo_sapiens.GRCh37.62.filter1.sorted.gtf > chr${i}_Homo_sapiens.GRCh37.62.filter3.sorted.gtf;
done
and then I combine in the "right " order with cat.

I am not sure yet how this could result into a corrupted gtf file.
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