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Question: Using DEXSeq count on a sliced bam or sam file
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gravatar for a.morris
12 months ago by
a.morris • 40
a.morris • 40 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 • 444 views
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modified 12 months ago by Jennifer Hillman Jackson ♦ 25k • written 12 months ago by a.morris • 40
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gravatar for Jennifer Hillman Jackson
12 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k
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