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Old 02-23-2017, 07:16 AM   #8
fanli
Senior Member
 
Location: California

Join Date: Jul 2014
Posts: 198
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Perhaps you have mixed up files in your script. You may want to check the logs in your tophat output directory.

As an example, here's what my align_summary.txt looks like:
Code:
Left reads:
          Input     :   6551998
           Mapped   :   5980941 (91.3% of input)
            of these:    199516 ( 3.3%) have multiple alignments (10560 have >10)
Right reads:
          Input     :   6551998
           Mapped   :   5574400 (85.1% of input)
            of these:    184354 ( 3.3%) have multiple alignments (10346 have >10)
88.2% overall read mapping rate.

Aligned pairs:   5394272
     of these:    177939 ( 3.3%) have multiple alignments
                  148603 ( 2.8%) are discordant alignments
80.1% concordant pair alignment rate.
and the corresponding prep_reads.info:
Code:
left_min_read_len=75
left_max_read_len=75
left_reads_in =6551998
left_reads_out=6544622
right_min_read_len=75
right_max_read_len=75
right_reads_in =6551998
right_reads_out=6495499
Note that both files refer to 6551998 as the number of read pairs input.
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