ShortStack

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Hi, I would like to point out that since version 1.3.0 bowtie does not support colorspace data. I think that this information should be updated in the manual, which says...

vojtace

Hi Mike, I have a question regarding the shortstack analysis from samples with a very different starting number of reads. In my analysis I have 4 different conditions, two of...

RubioB

Dear Dr. Axtell, I have just finished sRNA analysis for Arabidopsis using ShortStack 3.3 (on cyverse.org). In order to identify different sRNA subclasses, I used the Arabidopsis sRNA loci file...

midhatubaid

Hi: I am currently using ShortStack to identify sRNA cluster. I am a litter confuse about the parameter '--pad'. for example, I set "--pad 200 ". Is that mean If...

dadadawei

Strandness of PhasiRNAs

4

Dear Mike, I am currently having an issue with how Shortstack defines strandness in the data. I would like to plot sRNA loci based on strandness, however most of them...

Stefano192

Problems with shortstack output interpretations

2

Hi ! I am a little confused concernaning the results obtained with shortstack. To sum up, I work with two conditions and in each of them I have three biological...

RubioB

ShortStack padding bug?

2

Dear Michael Axtell: According to the README the pad parameter can be an integer between 0 and 50000. “Must be an integer between 0 and 50000. Default: 75". But whenever...

bbermudez

Bug: some reads are not placed in clusters properly according to pad/mincov

1

Dear Mike, We found that a small fraction of reads are not properly placed in clusters. I have a small reproducible example for you. ShortStack --nohp --pad 1 --mincov 1...

ceiabreu

only one read mapped

1

Hi Felix, I have a soybean sRNA-Seq data which I already used in the past with ShortStack to detected miRNAs. Now I want to run it without --locifile so it...

DiegoZavallo

Degraded mRNA

1

This may not be an appropriate question for the github issues section, however the Shortstack paper does say that for their mouse small RNA library many of the sRNAs had...

signor-molevol