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Old 03-23-2015, 01:03 PM   #14
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Originally Posted by rodf View Post
Hi Brian,

I'm using the Mira assembler to assemble Illumina MiSeq reads I got from NCBI/SRA. I use "fastq-dump --split-files -F xxxx.sra" to extract the reads and get two files. Each set of paired end reads have exactly the same name, and mira needs the /1 and /2 added onto the reads and gives an error if it detects reads with the same name.

Thanks for your quick reply,

You can now use the flags "addslash=t slashspace=f" together to accomplish that.

As an unrelated note, reformat now supports the "stoptag" flag, so it can process a sam file and add the stop coordinate of the read to the optional tags, prefixed by "YS:i:".
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