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junchaoshi / sports1.1

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
GNU General Public License v3.0
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pirna annotation #11

Closed QingLuo90 closed 3 years ago

QingLuo90 commented 3 years ago

Hi there,

The final output of all piRNAs are labeled the same as "piRNA". Is there a way to include the piRNA id?

junchaoshi commented 3 years ago

Hi,

The id for piRNA somehow is meaningless. Sometimes the ids are contradictive with each other among different databases. In this case, you can just name them using unique ids in your work.

QingLuo90 commented 3 years ago

Hi Junchao,

Thanks for replying promptly. Since the piRNA database has a lot of annotation info which is using the same id. I think things would be easier if the ids can be kept.

Best, Qing

Qing Luo, PhD student Biomedicum B5 Dept. Physiology and Pharmacology Karolinska Institutet SE-17176 Stockholm Sweden Phone: +46 (0)704028006

From: junchaoshi notifications@github.com Reply-To: "junchaoshi/sports1.1" reply@reply.github.com Date: Tuesday, 8 December 2020 at 20:44 To: "junchaoshi/sports1.1" sports1.1@noreply.github.com Cc: Qing Luo qing.luo@ki.se, Author author@noreply.github.com Subject: Re: [junchaoshi/sports1.1] pirna annotation (#11)

Hi,

The id for piRNA somehow is meaningless. Sometimes the ids are contradictive with each other among different databases. In this case, you can just name them using unique ids in your work.

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fork16 commented 1 year ago

@junchaoshi Hi Junchao, pirbase provides version 3.0 now, with more piRNAs and unique IDs; If this ID is used to anno, the software will analyze piRNA very well.

junchaoshi commented 1 year ago

Hi,

It is possible to use the updated pirbase as a reference. You may use parameter -w [pirbase file] without .fasta suffix as an input. For example:

-w mmu.v3.0

The piRNA ID information is contained under bowtie format in the intermediate [_processed] folder if parameter -k is applied. However, the id information would not be included in the final output since we are still concerning if it makes sense to annotate a single piRNA. Hope the information helps.

Junchao