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Hi,
I was trying to replicate your results using same set of fastq files as your paper used.
But I failed to reproduce the same trend of results. I was wondering what specific parameters you used …
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The install steps for src/hisat2.mk, src/fastp.mk, and src/salmon.mk are missing their corresponding namesakes: hisat2, fastp, and salmon
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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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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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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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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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```
##############################################################################
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###
### Running command:
###
### /ho…
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/home/shared/hisat2-2.2.1/hisat2 \
-x ../output/cgigas_uk_roslin_v1_genomic-mito.index \
-p 4 \
-1 ../data/F143n08_R1_001.fastq.gz \
-2 ../data/F143n08_R2_001.fastq.gz \
-S ../output/F143_cgigas.…
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Hi,
I am attempting to run DegNorm on some human RNA-seq data that I aligned using hisat2. It is able to load the files and the GTF, but consistently gives me the error below after it starts loadin…
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when running vanilla pepatac, I got this message.
Is there a way to streamline this? Like, maybe aggregate these and then print one list instead of duplicating the message?
```
## [1 of 16] sam…