I saw this in the latest issue of nature biotech: http://www.nature.com/nbt/journal/va.../nbt.3122.html. Here is the site for it: http://ccb.jhu.edu/software/stringtie/. Has anyone used this on their data yet? If so what did you think? I'm trying to estimate isoform abundance in my RNA-seq data.
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It looks pretty good from the paper, and I'd definitely give StringTie a shot, but I've not tested the software yet. However, if you're looking to try out a new tool, I'd also take a look at the Bayesembler (http://genomebiology.com/2014/15/10/501). It seems to have a very nice and principled probabilistic model that it uses to jointly infer what transcripts are present and quantify their abundance.Last edited by robp; 02-26-2015, 05:46 PM.
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Hi folks,
Sorry for bumping an old thread but I am facing this weird output from StringTie and thought you could spot the issue.
I am running StringTie on STAR returned BAM files (I have used the option to insert XS tag in SAM/BAM fields)
I have now run StringTie on 6 samples and in each I have the same scenario -
FPKM value as "inf" or "-nan"
StringTie returns a GTF file and this an example of the 9th col for one transcript -
gene_id "STRG.67"; transcript_id "STRG.67.1"; reference_id "ENST00000447513"; ref_gene_id "ENSG00000157911"; ref_gene_name "PEX10"; cov "1.525000"; FPKM "inf";
This is the cmd I am using
/path/to/stringtie-1.0.4/stringtie \
Aligned.sortedByCoord.out.bam \
-o StringTie_out/StringTie.gtf \
-p 16 \
-G /path/to/Homo_sapiens.GRCh37.73_Only-REF.gtf \
-B \
-e
Any hunches? I am sure I am doing something stupid but can't figure out what.
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hi everyone,
I figured out the stupidity and that was -not reading the manual properly :-(
The Manual page says -
..If you run StringTie, and all FPKM values that were produced appear to have the value inf then it is very likely that the HI tag starts at 1. An easy command that you can run...
So STAR out BAM files have the HI tag starting from 1 and hence.
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