STAR/StringTie compatibility on tag HI in the BAM alignment file
Hi, I am trying to do transcript reconstruction and quantification using StringTie on BAMs generated by STAR. According to https://ccb.jhu.edu/software/stringtie/#install, modifying the tag HI in the BAM alignment file to start at 0 (as previously required with STAR produced alignment files) is no longer needed starting at v1.1.0 release 10/19/2015. I came across this after having generated BAMs using STAR with --outSAMattrIHstart 0 option. And StringTie finished successfully using the BAMs generated by STAR. I'm really concerned if there are any underlying mistakes doing so. Thanks!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Error on rsem-calculate-expression
written by billyconan6a •
-
Very low read counts for PD1 when using STAR aligner compared to BWA
written by emi •
-
Bulk RNA-Seq pipeline suggestion incorporating UMIs
written by steveh •
-
Annotae with Transcript IDs for the chromosome coordinates in SJ.ou.tab files generated bu STAR ali…
written by akhan •
-
Does StringTie need strand information if HISAT2 was run with strand-specific information
written by piyushjo
-
Problem with generating BAM files with STAR
written by gokberk
-
STAR index doesn't finish
written by alvarocentron91 •
-
Adding tag XS to HISAT2 sam files perior to StringTie
written by Farbod
-
StringTie "missing header error" [for both HISAT2 and STAR alignment files]
written by EagleEye
-
Using StringTie with DESeq2(StringTie geneID and corresponding Ensembl geneID)
written by Megan •
