I have use HISAT2 for alignment . Now i want to obtain contig sequence from from BAM file in galaxy server?
I have used Samtools View. That is giving me some sequence but I am not sure whether it is contig or not?
I am a bit doubtful about what you are doing or wanted to do is correct. Please refer to some good reference articles or ask someone in your group who could understand the actual problem.
Since you used HISAT2, I am assuming you are analyzing RNA-seq reads. If you are trying to assemble transcripts from your BAM file, you should use something like StringTie.
if you want to extract the contig sequence, you can use the samtools software according to the contig sequence posisitions which you want to extract.
Alex Zaccaron Yes i am analyzing RNAseq reads. i don't want to assemble transcripts. I want to obtain contig sequence or consensus sequence form aligned BAM file sing a tool on galaxy server. can you recommend me ?
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