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Old 09-12-2012, 06:55 AM   #1
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Location: athens, ga

Join Date: Jul 2012
Posts: 8
Default Inquiry: minimum length of reads for referece-based assembly or de novo assembly

Hi all,

While doing QC preprocessing of RNA-seq reads, what could be the minumum length of reads for a reliable assembly: reference-base or de novo assembly?

I am a greenhand in RNA-seq area, and just wonder, when we met bad quality data, to what extent could we trim the reads?

for example, as fastqc results shown in the attachment.
Do I have to trim the first 10bps and the last 20bps?
Is 50bps left enough for (tophat->cufflinks) assembly?

Thank you very much in advance!!!!!!
Attached Images
File Type: png per_base_quality.png (9.8 KB, 14 views)
File Type: png per_base_sequence_content.png (25.8 KB, 7 views)
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Old 10-04-2013, 10:28 AM   #2
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Location: San Jose, CA

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Did you get a new insight on this problem? I posted a similar question here:
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