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Forum: Bioinformatics 07-05-2016, 07:13 AM
Replies: 2
Views: 2,303
Posted By asapp
Question resolved

Question resolved
Forum: Bioinformatics 07-05-2016, 06:44 AM
Replies: 2
Views: 2,303
Posted By asapp
OrthoMCL Pairs no output

Hello,

I'm trying to run the OrthoMCL pipeline and haven't had any issue until the OrthoMCL Pairs step. I have a SimilarSequences table in my MySQL database, a config file that correctly specifies...
Forum: Bioinformatics 10-03-2015, 11:49 AM
Replies: 0
Views: 3,183
Posted By asapp
STAR segmentation fault (--genomeSAindexNbases not reassigning?)

Hello!

I have used STAR successfully in the past to align with large reference genomes. I am now trying to align with a small genome (~3230 bases). I am using STAR v. 2.4.1d (and have tried the...
Forum: Bioinformatics 07-24-2015, 05:18 AM
Replies: 2
Views: 1,948
Posted By asapp
Perfect, thanks!

Perfect, thanks!
Forum: Bioinformatics 07-23-2015, 01:02 PM
Replies: 2
Views: 1,948
Posted By asapp
Intersecting multiple bed files

Hello,

I have several RNA-Seq transcript data sets assembled and in BED format. I have masked out previously identified transcripts from the data, leaving me with "unidentified" transcripts. A...
Forum: Bioinformatics 07-11-2015, 11:26 AM
Replies: 0
Views: 1,309
Posted By asapp
question about cufflinks masking

Hello all,

I recently created a merged.gtf file using cuffmerge. I want to mask all the known transcripts in this file when using cufflinks to search for novel transcripts at a particular locus...
Forum: Bioinformatics 07-10-2015, 06:00 AM
Replies: 2
Views: 2,281
Posted By asapp
Good to know, thanks so much! -Anna

Good to know, thanks so much!
-Anna
Forum: Bioinformatics 07-10-2015, 05:23 AM
Replies: 2
Views: 2,281
Posted By asapp
Cuffmerge error file never signals "done"...is this normal?

Hello all,

I'm fairly new to the bioinformatics world and am trying to combine several gtf files with cuffmerge. My shell script is as follows:

#!/bin/bash
...
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