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Old 01-14-2014, 03:07 AM   #1
Location: Münster, Germany

Join Date: Mar 2013
Posts: 42
Default 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
Thias is offline   Reply With Quote
Old 01-15-2014, 05:56 AM   #2
Location: Münster, Germany

Join Date: Mar 2013
Posts: 42

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.
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Old 02-19-2016, 07:32 AM   #3
Junior Member
Location: France

Join Date: Nov 2012
Posts: 1

thanks man...googling led me here! ...just the question i was seeking
afiseha is offline   Reply With Quote

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