-
**Hello, I tried to generate ref index using STAR with this code;**
_#!/bin/bash
/truba/home/user/STAR-2.7.7a/source/STAR --runThreadN 16 \
--runMode genomeGenerate \
--genomeSAsparseD 2 \
…
-
**Describe the issue**
Unsure if this is an issue or if I just messed up the input format. Tried running the metapipeline with a single donor, tumor normal pair but it errored out with "input CSV doe…
-
Hi,
I am trying to extract SNPs using hisat2_extract_snps_haplotypes_VCF.py script from Ensembl VCF file (ftp://ftp.ensembl.org/pub/release-87/variation/vcf/danio_rerio/Danio_rerio.vcf.gz) to build…
-
Hi,
I have downloaded Phylophlan version 3.0.60 via conda and following example 1 (S.aureus) tutorial on github.
This is the command I am using:
` phylophlan -i input_genomes -d phylophlan --d…
-
Hi all,
I'm new to this subject, and I guess I have a very basic question.
I have my transposon mutant library, and I want to visualize the mapped transposon insertions to the reference genome v…
-
Hi,
I have tried using the toSBGN() function to convert a BioPAX file into a SBGN representation, but I get the following error when I use it with your example data:
```
outFile
-
Hello,
I am interested in generating a track that summarizes (using color code) the number of nucleotides aligning at each position. In essence it would be identical to the track that is automaticall…
-
Hi, I tried running the pipeline and got this error:
Killed
(ERR): hisat2-align exited with value 137
[E::aux_parse] Incomplete aux field
samtools view: error reading file "-"
samtools view: er…
-
**Copy and paste the exact command you tried to run**
```
flair correct \
-q ERR10859992.bed \
-j data/shortreads_SJ.out.tab \
-g data/Ovis_aries_rambouillet.ARS-UI_Ramb_v2.0.dna.toplevel.f…
-
Big fasta files are common. I just ran into one that would require 14GB of RAM to read into R using `ape::read.dna`. I need a way to read into subsets of large fasta files.
The following should be p…