Transcriptome assembly with STAR or HISAT

[luigra]

Dear Geo,

I had different assembled transcriptomes depending by the usage of STAR or HISAT2 with the latest version of stringtie. You can see a screenshot of a region I am interested in.

Is there something that I need to do, other than sorting the bam by coordinates, in order to have a reliable transcriptome by using the alignment results from star?

Thanks in advance Luigi

Below you can find the command I used for it: /home/cbrcmod/scratch/modules/out/modulebin/stringtie/1.3.3/bin/stringtie /scratch/cbrc/analysis/BPepi-22/out/bam/STAR/ERR878367.sorted.bam -o /scratch/cbrc/analysis/BPepi-22/tmp/stringtie/ERR878367.gtf -p 6 --rf -G /scratch/cbrc/ref/ensembl/human/GRCh37.75/blueprint/Homo_sapiens.GRCh37.75.chr.gtf -v -l BPSTRG

/home/cbrcmod/scratch/modules/out/modulebin/stringtie/1.3.3/bin/stringtie /scratch/cbrc/analysis/BPepi-27/out/bam/hisat2/ERR878367.sorted.bam -o /scratch/cbrc/analysis/BPepi-27/tmp/stringtie/hisat2/ERR878367.gtf -p 8 --rf -G /scratch/cbrc/ref/ensembl/human/GRCh37.75/blueprint/Homo_sapiens.GRCh37.75.chr.gtf -v -l STRG

If can help I noticed that stringtie 1.2.3 on the star alignment was able to detect the new 5' exons and the longer 3 utr exon alongside with other transcripts (I included the relative track in the screenshot). This i the commands I used for it: stringtie /opt/data3/Projects/BPepi/BPepi-8/out/bam/STAR/ERR878367.sorted.bam -o /opt/data3/Projects/BPepi/BPepi-8/stringtie/MK/ERR878367/first_transcript.gtf -p 4 -G /opt/data2/mak58/blueprint/annotation/Homo_sapiens.GRCh37.70.gtf -v