mafTools
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dentearl
Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
cd mafValidator && make all make[1]: Entering directory `/share/zhangyuxin/mafTools/mafValidator' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/share/zhangyuxin/mafTools/mafValidator' cd mafPositionFinder && make all make[1]: Entering directory `/share/zhangyuxin/mafTools/mafPositionFinder' make[1]:...
Hello, I need to create an anaconda environment using the compiled tools in this repository. I'd like to know if it is possible for me to create an anaconda package...
Hello, Is there a way to specify the conversion from MAF to fasta be in chromosome order please, e.g. via the sequence used as reference? Or is this something that...
In the MAFComparator readme B~A is defined as a proxy for the _specificity_ (true negative rate) where I am wondering whether this measure might actually represent the _precision_ (positive predictive...
Hello, I have been trying to extract aligned fastas from a very large maf file (~64G) that contains 45 aligned whole genome sequences. When I try to run mafToFastaStitcher, I...
I am trying to use mafToFastaStitcher with a maf and set of fastas that I have generated using biopython (attached). However, I get the following error: Error, unanticipated character in...
Hi, Dentearl, When running mafToFastaStitcher, I came across the errors like this: Aborted (core dumped). I spent a lot time troubleshooting, but failed. Is there any solutions to this. Thank...
Hello, I generated a MAF file of genomes using Mugsy. By executing /usr/local/mafTools/bin/mafToFastaStitcher --maf ../output_mugsy/tmp.maf --seqs 10263_7_02,10263_7_44,10395_8_09,10395_8_30,10395_8_54 --breakpointPenalty 5 --interstitialSequence 20 --outMfa output.mfa I get this error: ERROR, file 10263_7_02...
I'm seeing some strange output in mafPairCoverage when looking at coverage in regions specified from a .bed file. It looks like In Regions and Out of Regions are reversed (which...
