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HI,gpertea.
Histat2 can add XS tag for all read alignments,I have a stranded library (fr-firststrand) data, I use STAR to mapping genome and set options --outSAMstrandField intronMotif which can add …
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It would be convenient if JBrowse could render spliced alignments from tabix-indexed GFF3 files using the CIGAR string in the GFF3 Gap attribute (e.g., produced from gmap's gff3_match_est format), rat…
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Hi Geo,
I have nanopore cDNA data aligned with minimap2 (with --cs --MD). I tried abundance estimation with StringTie v1.3.5 that should recognize the "CS" tag as an alternative to "XS". The splice…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
3.8.10 (default, Mar 15 2022, 12:22:08)
[GCC 9.4.0]
CPython
Linux-5.13.0-48-generi…
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Dear,
I want to run the PASA alignment assembly pipeline using a very genome which has very long trons such as longer than 20kb. I run the pipeline, some errors occur, I want to know whether this err…
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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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**Description:**
Add a dry-run mode to validate input parameters and configurations without executing the entire pipeline. This will help users verify their setup before running the full pipeline.
…
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Hello, I have a bam file where my reads are aligned to the `GENCODE GRCh38.p14.genome.fa file`.
The corresponding gtf file is `gencode.v44.chr_patch_hapl_scaff.annotation.gtf`
I tried running BAM…
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Hi Alevar! I was just looking at your beautiful code and I am quite curious as to what HIV data you used as each of the parameters and if you could link them. I want to see what each of the files look…
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Several present at the [Dec 2018 meeting](https://github.com/riboviz/bbsrc-nsf/blob/master/docs/minutes/20191203-Dec2019meeting.md), argued that genome-centric alignment is good for quality control an…