ShortStack

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I am trying to use shortstack for de novo miRNA discovery, and have little experience with small RNA. When I run the software, only ~33% of my reads map: Uniquely...

SaelinB

Hello, Dr Axtell. I have two batches of data, both of which are of the same species, and I ran two separate analyses to get two results files. But I...

aayoungfish

Update ShortStack

1

fix div 0 error

y9c

ShortStack adds three custom tags to BAM files that it creates .. these custom tags should be described in the README.

MikeAxtell

how to reserve the U&P reads of alignment bam file?

1

Hi Mike, I used ShortStack4 aligned my sRNA reads to genome, and I got the alignment_details.tsv and many bam files. And I have annotation file predicted by other softwares, so...

Yuzhang0102

Better reporting of read trimming

1

It would be nice if the `--autotrim` process provided a nicer summary of the results of read trimming .. preferably one which is easy to use to create plots by...

MikeAxtell

Low number of miRNAs identified

4

Hello! So I’m trying to use ShortStack for miRNA identification from sorghum roots samples. In order to test the efficiency of our small RNA library protocol we initially sequenced a...

rmr74370

Alert of syntax warning

3

Hi, Not really a blocking issue yet, just a warning on a bad syntax: SyntaxWarning: invalid escape sequence '\s' It occurs on 12 lines, running under python 3.12.3 (ShortStack was...

nponts

Errors will report which libraries failed to find adapters (may be multiple), and then specifically which library the processing pool failed on.

Aez35

siRNA analysis using ShortStack

8

Hello, Thankyou so much for developing such a versatile all in one software for analysing small RNAs I am using ShortStack for the small RNA analysis in my plant sRNAseq...

baibhav-bioinfo