Generating chrsize.tsv?

[Zhaozhe Hao]

Hello, 

Thank you for the great software and the detailed instruction! 

I have now installed the software and get things running for the toy genome.

When it comes to the real genome, there are two questions that it is hard for me to solve by myself.... Could you please give me some advice?

1)  How could I get the chrsize.tsv? I have downloaded the genome from NCBI toplevel.fa . But could not find the chrsize. tsv... Could you please give me some direction on how to generate them? We working on a rare species that UCSC does not have a table yet....

2) I am building the files for the Blacklist for analyzing scAtac-seq data. scAtac-seq are sequencing pair-ended 75 bp? so about 50 bp after trim? Should I use PE50 for the k-mer then?

Thank you,

Zhe

[Mehran Karimzadeh]

Hello Zhe,

chrsize.tsv is a tab delimited 2-column file, corresponding to chromosome name and size.

You can generate it by runnings samtools faidx <fasta file> and subsetting the output so it only contains such data.

If you are using paired-end data and each pair is 50 bp, you can use k-mers corresponding to the minimum span and maximum span of the fragments captured by paired-ends.

For example, if there is no overlap, the minimum span is 100 bp, and if the most largest paired fragments are 200 bp, you can use that as your maximum range.

You can look into the manuscript for an example of paired-end data we looked into.

Good luck,

Mehran

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[Zhaozhe Hao]

Thank you for the help, Mechran!