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Old 02-17-2014, 10:21 AM   #1
Location: USA

Join Date: Nov 2012
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Default Assembly using Illumina Paired-end reads from SRA with MIRA


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 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 ???) 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 ...
chayan is offline   Reply With Quote
Old 02-17-2014, 10:51 AM   #2
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Location: Halifax, Nova Scotia

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use the MIRA mailing list for quick and accurate response
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Old 02-18-2014, 01:24 PM   #3
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
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But first, search the mira_talk mailing list as people have discussed using SRA data there before.

Last edited by maubp; 02-24-2014 at 02:40 AM. Reason: Fixed autocorrected typo
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Old 02-24-2014, 01:36 AM   #4
Location: USA

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