Hi guys.
I successfully ran Solid data (50 bp reads) with current bowtie and tophat versions. But surprisingly it gave the following stats. especially only 21% aligning results!. Any one have any idea why aligning failed miserably ?
The command I used
Following is the tophat log file description
I successfully ran Solid data (50 bp reads) with current bowtie and tophat versions. But surprisingly it gave the following stats. especially only 21% aligning results!. Any one have any idea why aligning failed miserably ?
The command I used
Code:
tophat -o RHE014_Tophat_Output -C --library-type fr-secondstrand --segment-length 50 /home/choijk/Software/bowtie-0.12.7/indexes/hg18_c SL001_R00089_RHE014_01pgx2_F3_3_1
Code:
$ cat filezqaMDd.log # reads processed: 97340093 # reads with at least one reported alignment: 20468407 (21.03%) # reads that failed to align: 76790363 (78.89%) # reads with alignments suppressed due to -m: 81323 (0.08%) Reported 34579945 alignments to 1 output stream(s)
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