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itmat / Normalization

RNA-Seq normalization and quantification pipeline
https://github.com/itmat/normalization/wiki
GNU General Public License v3.0
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problem with quantify_genes.pl #29

Closed e-manduchi closed 10 years ago

e-manduchi commented 10 years ago

Hello, in my last run of the pipeline part2 (yesterday) I got the following error:

Use of uninitialized value $gene_tag in numeric eq (==) at /gpfs/fs121/h/manduchi/Normalization/norm _scripts/quantify_genes.pl line 51

By looking at the script I see that this is how $gene_tag is defined:

$gene_tag = $a[5];

but it appears to me that the input file leading to @a has 5 columns, not 6. Shouldn't $gene_tag be set to $a[4]? I have used this part of the pipeline before without problems, so I'm not sure if maybe the code was recently modified at that line. Thanks

e-manduchi commented 10 years ago

P.S. From the history it does appear that the line $gene_tag=$a[5] was recently added.

eunjijunekim commented 10 years ago

Thanks for reporting the bug. I am working on the issue and will let you know when it's ready.

eunjijunekim commented 10 years ago

The new version(v0.5-beta) is now available.