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cpockrandt edited this page Jan 31, 2021 · 15 revisions

Here is a list of (what we believe might be) frequently asked questions. If we are wrong and your questions remain unanswered, please open an issue on GitHub ☺️

Input

Alignments

  1. Where did you get the whole-genome multiple sequence alignments from to compute tracks?

    TODO

  2. Can I use such an alignment to score other species (not just the reference species)?

    TODO

  3. Can I use compressed alignment files?

    PhyloCSF++ uses memory-mapping and processed each file in parallel. Hence, it is not possible to use compressed input files. For the same reason you cannot use process substitution to redirect the output of a command as input (e.g., phylocsf++ ... <(create alignment)).

  4. Does it make a difference whether I pass multiple alignment files or a single file that contains all alignments?

    For tracks the output will be exactly the same. For scoring entire alignments, the only difference will be that a file with score is written for every input file. There is however an important difference for both tracks and regions: PhyloCSF++ parallelizes over the alignments in each file, not over all files. To get the best speed-up from parallelization, a file should have a significant amount of alignments in it. The worst thing that could happen, if you have one file for each single alignment, then no parallelization will happen.

Models

  1. New models have been uploaded to the original repository. Can I use them?

    TODO

  2. How can I compute models for my own set of species?

    TODO

  3. Why do I need the genome length and coding regions to create smoothed tracks?

    TODO

  4. How do I get the coding regions for the smoothened tracks?

    TODO

Output

  1. What do I need to do with the computed tracks?

    If you want to load your tracks into a genome browser, you usually want to index them first, i.e., convert the wig files into bw files. For this you can use wigToBigWig. wigToBigWig will ask for a chrom.sizes file, a file that contains the sequence length for each chromosome/sequence. You can parallelize the converting:

    find . -name '*.wig' | parallel --will-cite -j10 'bwFile={}; bwFile="${bwFile:0:-3}bw"; wigToBigWig {} hg38.chrom.sizes $bwFile'

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