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Forum: Bioinformatics 07-03-2015, 05:35 AM
Replies: 3
Views: 1,992
Posted By annaprotasio
As expected, the problem was in the GFF file. ...

As expected, the problem was in the GFF file.

It was probably me just not reading/interpreting the directions properly, but I suspect this could happen to other people as well.

Be aware that:...
Forum: Bioinformatics 07-03-2015, 02:56 AM
Replies: 6
Views: 1,409
Posted By annaprotasio
hi Dan, Have a look at "samtools flagstat" ...

hi Dan,

Have a look at "samtools flagstat"

The output will looks something like this and I think it contains all the info you requested.

7276199 + 0 in total (QC-passed reads + QC-failed...
Forum: Bioinformatics 07-03-2015, 01:59 AM
Replies: 3
Views: 1,992
Posted By annaprotasio
Hi Blancha, Thanks for your comments. ...

Hi Blancha,

Thanks for your comments.

Agreed, the bam and gtf files do look different. But these are only the ten first lines of the files. Both the bam and the gtf have the information for...
Forum: Bioinformatics 07-02-2015, 09:10 AM
Replies: 3
Views: 1,992
Posted By annaprotasio
dexseq-count.py DEXSeq gives no results

Hello,

I am running into a bit of a problem with dexseq-count.py from DEXSeq.

dexseq-count.py. was installed and it runs OK with the sorted bam file and the gtf I provide (see below) but there...
Forum: Bioinformatics 11-19-2014, 04:57 AM
Replies: 6
Views: 6,146
Posted By annaprotasio
Hi, just wanted to say that this thread really...

Hi,
just wanted to say that this thread really helped sorting out my trimmomatic call.

I have smallRNA libraries and due to their nature, a big proportion of the read is adapter. I was running...
Forum: Bioinformatics 03-02-2011, 04:52 AM
Replies: 12
Views: 6,795
Posted By annaprotasio
Question Goseq for non-native goseq db

hi

I am new to Goseq and I am trying to implement it for a genome not present in the database. I have the list of genes and their associated GO terms. It's just that it's not clear to me how can I...
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