marginAlign
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benedictpaten
UCSC Nanopore
I am attempting to install marginAlign into a cluster environment utilising the lmod modules system (so I suppose I am also echoing alanorth's request to please tag your releases in...
Hello, I am trying to use marginStats to collect alignment stats from minimap2 aligned data of a direct RNA sample, this error is reported: ``` ... Detected a discrepancy between...
Hi there, Attempting to run marginCall on a .sam produced by minimap2. Built according to readme (using a venv) and all tests passed. Getting the below error, any ideas? The...
Hello, I am trying to **use MarginAlign with the last release of Minimap2** (`2.15-r908-dirty`) and I had several issues: 1) I had this mysterious PySam error, that has not yet...
It's difficult to install this system wide in a cluster environment because it doesn't have a proper version. Right now I'm just using versions like `marginalign/git-2369dafd` with the commit hash...
To write this up we need to record runtimes for how long it takes (wall and processing time) to process a minion dataset, both for marginAlign and marginCaller. I think...
Hi, Can we use .fasta as input read files? Is it hard-coded to work only with only .fastaq files as input? If yes, where is the code for that?
Hello, I am running marginAlign and used `--maxThreads 90`, however the process `lastal` is only using one thread. Is this normal? What parts of marginAlign are parallelized, and is the...
Hi, Thanks for the marginAlign suite. It is great. I was wondering if there was a way to have marginStats (or other approach) go through alignments and spit out the...
Hi there, I used marginAlign and marginCaller to analyse my data. I just wonder if the VCF format generated by marginCaller can be converted into normal format. That will make...
