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Forum: Bioinformatics 07-17-2011, 10:34 AM
Replies: 6
Views: 2,900
Posted By jjpurwar
I figured out the solution to my problem. Turns...

I figured out the solution to my problem. Turns out that my sam file header had to be in the right format:

The first line needs to be header.
The second line needs to be a dummy read group line...
Forum: Bioinformatics 07-17-2011, 10:32 AM
Replies: 3
Views: 4,809
Posted By jjpurwar
I figured out the solution to my problem. Turns...

I figured out the solution to my problem. Turns out that my sam file header had to be in the right format:

The first line needs to be header.
The second line needs to be a dummy read group line...
Forum: Bioinformatics 07-16-2011, 07:14 PM
Replies: 6
Views: 2,900
Posted By jjpurwar
How did you resolve this issue? Please help!

How did you resolve this issue? Please help!
Forum: Bioinformatics 07-16-2011, 07:13 PM
Replies: 3
Views: 4,809
Posted By jjpurwar
Hi - I received the same error. I also reheadered...

Hi - I received the same error. I also reheadered my sam file and then tried to convert to a bam and received the [sam_read1] reference 'chrX' is recognized as '*'.

Did you ever figure out a...
Forum: Bioinformatics 06-27-2011, 05:48 PM
Replies: 5
Views: 2,272
Posted By jjpurwar
Figured a fix for this - the segment-length needs...

Figured a fix for this - the segment-length needs to be set to atleast half of the read length. else junctions wont be reported.
Forum: Bioinformatics 06-27-2011, 08:44 AM
Replies: 5
Views: 2,272
Posted By jjpurwar
Im having the same issue. Interestingly, when my...

Im having the same issue. Interestingly, when my input file has reads that are 50 bp, my *.bed files are NOT empty. However, when using a 36 bp input file, the *.bed files are empty.
Any clues on...
Forum: Bioinformatics 06-22-2011, 09:02 AM
Replies: 5
Views: 7,510
Posted By jjpurwar
Hi, so I did specify the --solexa1.3-quals as my...

Hi, so I did specify the --solexa1.3-quals as my option. I dont take for granted the default option.
I did check with tophat regarding this matter - turns out that they dont take mapping qualities...
Forum: Bioinformatics 06-22-2011, 09:00 AM
Replies: 5
Views: 7,510
Posted By jjpurwar
Hi, so I did specify the --solexa1.3-quals as my...

Hi, so I did specify the --solexa1.3-quals as my option. I dont take for granted the default option.
I did check with tophat regarding this matter - turns out that they dont take mapping qualities...
Forum: Bioinformatics 06-21-2011, 04:21 PM
Replies: 5
Views: 7,510
Posted By jjpurwar
Smile mapping quality score in tophat sam file

Hello all,


I have been trying to work with the sam output file that I received from tophat. My input file was an RNA-sequencing single end 36 bp run using Illumina GA2 with C. elegans data.

A...
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