Question: Genome guided assembly using hisat2 and StringTie
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gravatar for Bioinfonext
2.6 years ago by
Bioinfonext160
Korea
Bioinfonext160 wrote:

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

rna-seq • 1.4k views
ADD COMMENTlink modified 2.5 years ago • written 2.6 years ago by Bioinfonext160

Hi, I am waiting for reply.....is anyone using Hisat2 and StringTie together.

Thanks

ADD REPLYlink written 2.5 years ago by Bioinfonext160
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