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Question: Tophat
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gravatar for 杨继文
6.7 years ago by
杨继文 • 210
杨继文 • 210 wrote:
Dear all, This might be a silly question, but I couldn't figure it out by myself :-((. Could you please tell me how I can find out how many reads have been mapped to the genome after running Tophat for pair end RNA seq data? Thanks in advance. JIwen
rna-seq tophat • 770 views
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modified 2.3 years ago by y.hoogstrate • 460 • written 6.7 years ago by 杨继文 • 210
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gravatar for Jennifer Hillman Jackson
6.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Jiwen, The tool "NGS: Picard (beta) -> SAM/BAM Alignment Summary Metrics" gives a nice set of statistics for paired end data. Hopefully this helps, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
ADD COMMENT • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for y.hoogstrate
2.3 years ago by
y.hoogstrate • 460
Netherlands
y.hoogstrate • 460 wrote:

I don't know how Tophat in Galaxy does this currently, but in CLI Tophat, unmapped reads were put in a separate BAM file making it hard/impossible to obtain statistics that involve unmapped reads.

Tophat in Galaxy should also produce a summary file that gives some basic statistics including the percentage mapped/unmapped reads. The file should appear in your galaxy history as e.g. "100 Tophat on data 16: align_summary"
ADD COMMENT • link written 2.3 years ago by y.hoogstrate • 460
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