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Hello!
First of all thank you for designing this tool. So far it has very useful / accurate on my datasets.
I would like to get some clarifications regarding the way isoquant count reads based…
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Hi
I have been using agat for two years for now and it has worked wonders. I have recently discovered that a new [RNASeq QC tool ](https://github.com/getzlab/rnaseqc) that requires a feature collap…
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Hi there,
Thank you again for helping me the other day with the issues I was having. I've been able to run bambu successfully on some of my samples, and I have a couple of follow-up questions (I ho…
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hello Roleren,
recently, I was adding some virus genes in human genome, I did it like add fasta sequence in human fasta and make some simple annotation info at the tail of gtf files, just like…
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If minimap2 is installed in a linux OS via `apt-get`, the executable is located at `/usr/bin/minimap2`, and so "k8 and/or paftools.js" are not located in that directory.
It appears that the linux …
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In put for example:
NC_048303.1 StringTie gene 90101184 90185752 . - . gene_id "DMRT1";
NC_048303.1 StringTie transcript 90101184 9…
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Hello,
I am a bit confused by my isoquant results. I analyzed three BAM files with combined 109932 mappings (109931 primary, 1 supplementary). The log shows that all 109931 reads were classified as…
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hi @andrewprzh
command : isoquant.py -d pacbio_ccs --fl_data --bam minimap2mappedsorted.bam --reference chromosomes.fa --output isoquant --threads 8 --transcript_quantification all --gene_q…
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Hello,
I'm working with Sorghum bicolor, and both my gene and TE annotation files were obtained from Phytozome as gff3 files.
I had no trouble converting the gene gff3 file to gtf format using gf…
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Hi
I have been trying for 3 days but still coulnd't get it work on my end. Sorry I have very little knowledge and training in bioinformatics so please bear with me with the basics. I had RNA-seq da…