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Question: parameters and library type for tophat
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gravatar for 1603.neha
2.6 years ago by
1603.neha • 70
1603.neha • 70 wrote:

hi i haev SRA ids on which i am working. i plan to generate a reference based assembly. 1. i have downloaded the data from ebi link. 2. Next i have done qc and groomed the sequences using FAstqc and Fastqgroomer. Now as i have seen the pipelines i am supposed to do tophat for mapping. 3. i want to know that which library type i should choose for my single end data. what should bet he mean inner distance between pairs? 4. i am using six SRA sequences. a m i supposed to run tophat separately on each? 5. how to analyse fastqc result? thanks a lot

rna-seq tophat parameters library • 822 views
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modified 2.6 years ago • written 2.6 years ago by 1603.neha • 70
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gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Library type: see this Which "Library Type" Should I Use For Single-End Reads If unknown, use unstranded

Mean inner distance: not an option for single end data

Job execution: run as multiple inputs or as a dataset collection

Other Qs: This tutorial should be of help http://usegalaxy.org/galaxy101

Best, Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for 1603.neha
2.6 years ago by
1603.neha • 70
1603.neha • 70 wrote:

hi thanks for the replies. i have checked the QC report.it says pass
ADD COMMENT • link written 2.6 years ago by 1603.neha • 70
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