Question: Using DEXSeq count on a sliced bam or sam file
0
gravatar for a.morris
24 days ago by
a.morris10
a.morris10 wrote:

Using DEXSeq count on a sliced bam or sam file does not seem to run properly. The output file reads eg., as follows: ambiguous 0 _ambiguous_readpair_position 0 _empty 9893 _lowaqual 0 _notaligned 0 The sliced file had the hg19 genome database .

rna-seq • 53 views
ADD COMMENTlink modified 24 days ago by Jennifer Hillman Jackson23k • written 24 days ago by a.morris10
0
gravatar for Jennifer Hillman Jackson
24 days ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

There are a few different human reference genome versions are being used with tools and assigned to datasets. These are not always a match for the actual database used (example: Tophat run against hg19 but the BAM is assigned to the database 'hg19Patch2" - which is not indexed for tools). Other times there is a mismatch between inputs or tool form settings. This is probably the root cause of your recent problems.

The same exact reference genome should be used for an entire analysis. If the mapping was run against hg19, then that should be set as the database, and all other inputs and tool form options should be based on hg19.

https://galaxyproject.org/support/ >> Mismatched Chromosome identifiers

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 24 days ago by Jennifer Hillman Jackson23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 114 users visited in the last hour