Including piRNA quantification in smallRNAseq pipeline

[mshadbolt]

Hi guys

More of a feature request than an issue but I was wondering if there is a reason why piRNAs aren't currently included in the smallrnaseq .gtf file (~/bcbio-nextgen/data/genomes/Hsapiens/hg19/srnaseq/srna-transcripts.gtf). It would be great if they were included as part of seqcluster quantification in the srnaseq pipeline.

thanks
Marion

[lpantano]

Hi, Thanks for the reminder. I removed that because the server was down, but I’ll add it again, you can change the hg19 manually by doing this: # wget http://www.regulatoryrna.org/database/piRNA/download/archive/v1.0/bed/piR_hg19_v1.0.bed.gz # zcat piR_hg19_v1.0.bed.gz | awk '{print $1"\t.\tpiRNA\t"$2"\t"$3"\t.\t"$6"\t.\tname "$4";"}' >> srna-transcripts.gtf I hope this help. Cheers

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On Jul 10, 2018, at 1:39 PM, Marion ***@***.***> wrote: Hi guys More of a feature request than an issue but I was wondering if there is a reason why piRNAs aren't currently included in the smallrnaseq .gtf file (~/bcbio-nextgen/data/genomes/Hsapiens/hg19/srnaseq/srna-transcripts.gtf). It would be great if they were included as part of seqcluster quantification in the srnaseq pipeline. thanks Marion — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[mshadbolt]

awesome thanks

[roryk]

Hi @lpantano,

I see v2.0 are out for these:

http://www.regulatoryrna.org/database/piRNA/download/archive/v2.0/

Do you think switching to 2.0 makes sense? I also see the archive is back up, so we could just turn it back on in cloudbiolinux. Which one do you think we should do?

[roryk]

Also, I see the hg38 piRNA installation is using the coordinates from hg19-- do we need to lift those over?