ShortStack

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Double tab in Counts.txt

2

Hi! I've noticed in the Counts.txt, unplaced sRNA have double tab between the _main_ and first condition column. `UUUUAUUAUGAUCCAUUUCGCGUGGAAUUCUGGGUGCCAAGGAACUCCAG NA 114 37 15 37 25 ` In this case, between...

juancresc

ranmax 1: avoid choosing primary alignment randomly at all

1

Dear Mike I find the u and f mmap assignments very useful, however, I would like to avoid assigning a multi-mapping read to a place where there’s no possible guidance,...

bbermudez

Separating the known miRNAs from the new clusters identified in ShortStack

3

Hi, As per the instructions, i have run the pipeline using the denovo-clustering and after which I provided the loci file of known miRNAs from miRBase. How am I supposed...

tarakaramji

How should we adjust the parameters according to the 2018 Criteria suggested in PlantCell

1

Dear ShortStack colleagues, Thanks for sharing this wonderful tool for analysis of small RNAs. According to the 2018 Criteria you published in www.plantcell.org/cgi/doi/10.1105/tpc.17.00851, I think it is difficult to adjust...

boya888

Inaccurate description of Counts.txt in the README

1

Description of Counts.txt in README is not accurate and needs to be updated.

MikeAxtell

Allow bowtie2 .bam file as --readfile option without realignment

1

Allow bowtie2 .bam file as --readfile option without realignment. Usage: ShortStack.pl --readfile myBowtie2file.bam --genomefile hg38.fa --inbam

zajakin

Corrected bowtie options

1

Corrected bowtie options

zajakin

Hi Mike, I got the following error and the ShortStack 4.0.3 stopped running: Traceback (most recent call last): File "/lustre/BIF/nobackup/ruite093/miniconda3/envs/ShortStack4.0.3/bin/ShortTracks", line 282, in if last_pos < chr_sizes[last_chr]: KeyError: 'foobarbaz' Candidates...

meerveld96

IndexError: list index out of range during "Screening of possible de novo microRNAs"

5

I'm getting the above listed error. This is odd, as I've actually run this successfully previously, with a different subset of the same input reads! If you happen to have...

kubu4

Dear Mike, I've noticed some discrepancies between the default settings outlined in ShortStack's documentation and the actual code: 1. In the documentation, `--mmap` is listed as defaulting to `f`, but...

spriego