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Hi, Gabe
I was trying to run NINJA-OPS on my Windows 10 BASH environment. I've got bowtie2 installed in the path and running ok. Here is the error message I got:
Any idea? Thanks!
Running NIN…
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I used CONSENT v2.0 to do nanopore long reads correction, but I encountered some problem all errors are core dump.
I traced the source code and found the function indexReads in utils.cpp is the probl…
87joe updated
4 years ago
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Hi -- for my line of work I often have to (de-)serialize bioinformatic file formats into more common formats, and I'm curious if there are any recommendations for how to do that with noodles or if som…
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Hi,
I am finding that maligner is returning no alignments when the maps are longer than circa 500 kb or so.
Here is an example using your provided example as a starting point.
I get all alignments b…
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Hello, I evaluated the LAI using results from de novo LTR identification and EDTA, but the LAI values from the two results differ significantly. I would like to know which result I should trust and wh…
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Check if input file is fasta or fastq since some tools cant process fasta files only (`fastqc, trimmomatic`) and some need special flags indicating the format e.g. `bowtie2`. Just check if the file pa…
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So, I have about 883 single-end read SmartSeq libraries without UMIs or cell barcodes in FASTA format that I have tried using manifest files and such, but ultimately, can only end up with a single rea…
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Hi,@natacha-beck !
I am trying to run MFannot locally, from docker-container. Am I right, that the only input format is the Masterfile? How can I get a Masterfile from nucleotide fasta?
I am runn…
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Hello,
I have a fasta file with below format, and like to have VDJ assignment based the reference (IGMT or IGBLAST) for each of the sequence. After running the abstar on my fasta file, no output gene…
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Hi Ian,
Thanks for making this great tool available!
I've been able to get this running in a Singularity container on my machine, but I would like to have output in GenBank format (I can't find an…