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mhammell-laboratory / TEtranscripts

A package for including transposable elements in differential enrichment analysis of sequencing datasets.
http://hammelllab.labsites.cshl.edu/software/#TEtranscripts
GNU General Public License v3.0
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Index name-sorted bam files. #99

Closed WeijiaSu closed 2 years ago

WeijiaSu commented 2 years ago

Hello, Thanks for the useful program. I am using bam files that are sorted by name (samtools sort -n), and the TEtranscripts showed error: [E::idx_find_and_load] Could not retrieve index file for XXX; But samtools can only index bam files sorted by position, I am wondering what kind of index file I should use for the name-sorted bam files? Thanks for your help. Weijia

olivertam commented 2 years ago

Hi Weijia,

This is a quirk of the newer Pysam module (see #82). It doesn't appear to affect the actual run of TEtranscripts. You could confirm this by looking for the output files (e.g. xxx.cntTable), and reading through the rest of the log once the run is done.

Thanks.