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7.2 years ago
Bioinfonext
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460
I map pair end reads to genome using Hisat2 and sam file was sort and converted in bam file.
After that I used this command for StringTie assembly:
/home/yog/software/stringtie-1.3.2.Linux_x86_64/stringtie -p 8 -G gene.gtf -o assembly.gtf -m 500 -v map.bam
It creates these following files:
1) assembly.gtf
2) t_data_ctab
3) i2t_ctab
4) i_data_ctab
5) e2t_ctab
6) e_data_ctab
then through gffread I extracted assembled fasta sequences, using reference.fasta
/gffread assembly.gtf -w transcript.fasta -g reference.fasta
Is it the right way to do genome-guided assembly using StringTie?
Can I get assembled fasta sequence directly from the above stringTie command?
Thanks in advance
Hi, I am waiting for reply.....is anyone using Hisat2 and StringTie together.
Thanks