Use SRR files with .rar (ziped) format

FelixKrueger / Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

http://felixkrueger.github.io/Bismark/

GNU General Public License v3.0

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Use SRR files with .rar (ziped) format #686

Open iranianuser opened 3 months ago

iranianuser commented 3 months ago

Hello I had trouble with uploading my read files in a sever to do Bismark analysis cause they are so big (about 20 G). I compressed them with winRar and I want to run Bismark alignment. Can I ran Bismark with .rar format reads? If I can't please tell me another way. Is there a way to change the format to gzip? thanks alot

FelixKrueger commented 3 months ago

Bismark generally takes files either as .fastq or its gzip compressed version .fastq.gz. winRar is not supported, and I would generally recommend to use a Linux or Mac environment for analysis. If you've for .sra files you will first need to transform them to FastQ format using tools such as sratools.