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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
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Stringtie Stuck on Chromsome21 #221

Open Liuy12 opened 5 years ago

Liuy12 commented 5 years ago

Hi,

I encountered similar errors as to issue #13 when running StrintTie version 1.3.3. StringTie basically stuck at a certain bundle for days. I looked at this region in IGV and it seems like this region has tons of duplication reads and multi-mapped reads (Over 15000). I guess this is the reason that causes stringtie to stuck at this position. I tried to use the -M option and set it to a relatively lower value (0.1), but that didn't help. I am wondering do you have any suggestions regarding this issue? Do I need to pre-filter the bam files to remove multi-mapped reads? Any suggestion is appreciated. Thanks

Yuanhang(Leo) Liu Informatics Specialist Division of Biomedical Statistics and Informatics

Mayo Clinic 200 First Street SW Rochester, MN 55905

gpertea commented 5 years ago

Read duplication and multi-mapping are not such big problems for StringTie as is a large number of junctions in a single locus/bundle. This might be one of those cases where a lot of possibly spurious junctions can slow down StringTie significantly and even cause memory exhaustion (see some discussion about this scenario here: https://github.com/gpertea/stringtie/issues/203#issuecomment-433091677). Some pre-filtering of your data can be attempted (if you can find ways to eliminate low-quality or otherwise unlikely alignments before feeding the alignments to StringTie), or you can try using a larger value for the -j option (e.g.: -j 3), which of course comes with the downside of reducing sensitivity for low-expression genes..