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I contacted the depositing scientists and recieved this answer, which I would like to post here in case someone else ever has the same problem:
The YLF files contain the 5' position of mapped reads. Unfortunately, we have retired the computational pipeline that uses .ylf files and do not have any converter code. [...]. SRA files should allow read mapping and downstream analysis. Thanks for your interest in our data.Leave a comment:
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Anyone has experience with .ylf (young lab format) files ?
Hello guys,
I am interested in viewing the ChIP-Seq results published in GSM722170. Apart from downloading the SRA and realigning the reads (which I would like to avoid of course), there is a .ylf file for download.
It is a text file with numbers, which could possibly represent chromosomal positions (although quite many occur multiple times). But I don't have any idea, how to easily awk this into a bed file. The website of the Young lab also does not offer any converter for download.
Therfore: Has anyone ever worked with .ylf files and could possibly recommend me a way how to convert them into a more common format ?
Best regards
Matthias
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