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Hi I am interested in hosting this workflow on a Cromwell-enabled platform, but I've been seeing errors even trying it locally with both the stable and develop branches using these inputs derived from…
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Hi again,
For Braker1, I had been providing BAM files produced by STAR.
Since you are now using StringTie assembly as part of the Braker pipeline, I was wondering if there are any notable perfo…
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I am running bam-readcount as part of an analysis of three samples. The first two finished in a few hours but the third has been running for 40h (with 100% use of one CPU) already.
`/usr/bin/bam-re…
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Good morning,
I am trying to launch `hisat2_extract_splice_sites.py `and `hisat2_extract_exons.py` (the latest versions):
```
#!/bin/bash -l
conda activate hisat2
cd .../ref_genome/
/home/…
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Hi
I use hisat2-build to build a index ， an error occur
Traceback (most recent call last):
File "/Users/Huiqiang/bin/hisat2-build", line 95, in
main()
File "/Users/Huiqiang/bin/hisat2…
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I find out that the --un flag will affect the performance of `hisat2`.
For example, in `hisat2ORF`, I run both
```
hisat2 -p 8 -k 2 --no-spliced-alignment --rna-strandness F --no-unal --un unalign…
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Hello,
I am trying to run hisatgenotype. I installed both hisat2/2.2.1 and hisatgenotype. Here's my exact command:
```
python3 /cluster/home/user/hisatgenotype/hisatgenotype --base hla --locus-li…
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Hi, I encountered an exception from make_a_table,py script (discard_non_unique_mappings function) when using BAM files from HISAT2/samtools/picard, where some reads have no NH tag. According to HISAT2…
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Hi,
I am getting following ERROR message while aligning my data.
command:
./hisat2 -f -x ../hisat-trt/PEDV -U ../clean_trt.fasta -S ../trt.sam
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ERROR:
File "/home/kumarm/allan-work/…
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Genome index built (with same version of hisat2 as used for alignment) using basic build cmd (as I've done many times before)...and without any errors. For what it's worth, the genome is highly fragme…