Assembly using Illumina Paired-end reads from SRA with MIRA

[chayan]

Hii

I have downloaded a Pair-end data set from SRA and used fastq-dump from SRA tool-kit to generate the fastq file for that..well everything works fine till here..now i wanted to reassemble it with MIRA..but from SRA i got only one file for pair end reads, as they mentioned that it will be a joined (may be by cat ???) file...now i am not sure how to a single file for a PE assembly with MIRA..somewhere i found that they mention it to use as a unpaired one but then should i use readgroup = unpaired/PE... in both cases MIRA is complaining...little confuse..any one has any experiences with this???

thanks for any help

best ...

[JackieBadger]

use the MIRA mailing list for quick and accurate response

[maubp]

But first, search the mira_talk mailing list as people have discussed using SRA data there before. http://www.freelists.org/list/mira_talk

[chayan]

thanks to both of you..yes, i got the answer from the mira-mailing list indeed