I used Tophat to map a RNA-seq paired-end data set and the samtools flagstat gives the following summary:
My question is why tophat gives me '0 + 0 with mate mapped to a different chr' ? I also used BWA to map the same data and it gives '1417632 + 0 with mate mapped to a different chr'. will Tophat ignore the pairs mapped with both end mapped to different chrs or there is something wrong with my settings for running tophat command?
here is my command:
The fragment length is 400bp, and reads are 100bp.
Code:
63211490 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 63211490 + 0 mapped (100.00%:nan%) 63211490 + 0 paired in sequencing 32750906 + 0 read1 30460584 + 0 read2 53967250 + 0 properly paired (85.38%:nan%) 58218754 + 0 with itself and mate mapped 4992736 + 0 singletons (7.90%:nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)
here is my command:
Code:
tophat -r 200 -p 4 -o RNA_seq seq1.fa seq2.fa
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