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Forum: Bioinformatics 11-09-2009, 02:03 PM
Replies: 2
Views: 2,030
Posted By spb2003
Thanks for the reply. I was going to add memory...

Thanks for the reply. I was going to add memory to my machine soon. I think now is a good time.
Forum: Bioinformatics 11-09-2009, 10:04 AM
Replies: 2
Views: 2,030
Posted By spb2003
Alloc error in Tophat

Hello All,

I have been running tophat on Solexa RNAseq data. A few times, tophat crashes for certain lane data with the following error:

Found 0 potential split-segment junctions
Indexing...
Forum: Bioinformatics 10-13-2009, 02:19 PM
Replies: 3
Views: 3,415
Posted By spb2003
for eg. I want to align...

for eg. I want to align CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA against two index files hg18_block1 and hg18_block2. Since I am still building the index, I will give an example using different index
...
Forum: Bioinformatics 10-13-2009, 09:52 AM
Replies: 3
Views: 3,415
Posted By spb2003
Multiple index files in Bowtie?

Hello Everyone,

I am working on a 32 bit RH Linux machine and setting up a RNASeq analysis pipeline. As part of ERANGE, I am building an index of the expanded genome but on including .fa.masked...
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