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ydLiu-HIT / deSALT

deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads
MIT License
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Strand information #29

Closed gmoneyomics closed 4 years ago

gmoneyomics commented 4 years ago

Hi. I am using deSALT to align nanopore cDNA and feeding the bams into StringTie2 for assembly and quantification. StringTie requires strands information in the bam file. Is there a way to add strand to the bam? Thanks!

ydLiu-HIT commented 4 years ago

Hi, I don't know about the strands information you pointed, is it the aligned read come from forward strand or reverse strand? If necessary, you can give me an example of the information in bam file. If feasible, I will add it to deSALT for you.

Best Yadong

gmoneyomics commented 4 years ago

Hi Yadong,

Thank you for getting back to me. We normally use the XS tag in the bam alignment, in the way that Hisat2 (or TopHat) reports it. Here is a description for it:

XS:A:

Values of + and - indicate the read is mapped to transcripts on sense and anti-sense strands, respectively. Spliced alignments need to have this field, which is required in StringTie. We can report this field for the canonical-splice site (e.g. GT/AG, GC/AG ), but not for non-canonical splice sites.

For instance, if the alignment will produce an intron starting with a GT and ending with an AG the tag XS:A:+ would be added to the bam entry. If it is starts with CT and ends with an AC then it will have the XS:A:- tag.

Thanks!

Ariel

From: ydLiu-HIT notifications@github.com Sent: Friday, May 8, 2020 10:16:00 AM To: ydLiu-HIT/deSALT Cc: Ariel Gershman; Author Subject: Re: [ydLiu-HIT/deSALT] Strand information (#29)

Hi, I don't know about the strands information you pointed, is it the aligned read come from forward strand or reverse strand? If necessary, you can give me an example of the information in bam file. If feasible, I will add it to deSALT for you.

Best Yadong

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ydLiu-HIT/deSALT/issues/29#issuecomment-625836742, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ALNHXECSGMSYAAFATISMIU3RQQH2BANCNFSM4M25DVBA.

ydLiu-HIT commented 4 years ago

Hi,

I am sorry to reply to you later. I have released deSALT-v1.5.4(https://github.com/ydLiu-HIT/deSALT/archive/v1.5.4.tar.gz) which has added "XS:A" tag, you can download directly and test the code. If there have any question, please tell me.

Best, Yadong

gmoneyomics commented 4 years ago

Hi Yadong,

Thank you very much!

From: ydLiu-HIT notifications@github.com Sent: Sunday, May 17, 2020 7:51:47 AM To: ydLiu-HIT/deSALT Cc: Ariel Gershman; Author Subject: Re: [ydLiu-HIT/deSALT] Strand information (#29)

Hi,

I am sorry to reply to you later. I have released deSALT-v1.5.4 which has added "XS:A" tag, you can download directly and test the code. If there have any question, please tell me.

Best, Yadong

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ydLiu-HIT/deSALT/issues/29#issuecomment-629784638, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ALNHXEAN3PG23445QSIXY6DRR7FVHANCNFSM4M25DVBA.