Question: what is wrong with samtools flagstat or read mapping?
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gravatar for rajeshkumar_vinod
2.6 years ago by
india
rajeshkumar_vinod30 wrote:

I have 6,673,385 reads in each pair end file after quality filtering. but when i map it using tophat and run i run samtools flagstat on bam file it gives following output

1343686 + 0 in total (QC-passed reads + QC-failed reads)

0 + 0 duplicates

1343686 + 0 mapped (100.00%:-nan%)

1343686 + 0 paired in sequencing

670808 + 0 read1

672878 + 0 read2

1203600 + 0 properly paired (89.57%:-nan%)

1311198 + 0 with itself and mate mapped

32488 + 0 singletons (2.42%:-nan%)

15874 + 0 with mate mapped to a different chr

452 + 0 with mate mapped to a different chr (mapQ>=5)

I am not very sure how to interpret samtools flagstat output, but as i assume there are only 670808 reads in pair1 are mapped 672878 from pair2. is it correct? That is 1/10 th of the total input reads. where are rest of my reads???

Report produced by tophat shows some other statistics

Left reads:

      Input     :    468668

       Mapped   :    443344 (94.6% of input)

        of these:    216780 (48.9%) have multiple alignments (1 have >20)

Right reads:

      Input     :    468668

       Mapped   :    444468 (94.8% of input)

        of these:    217699 (49.0%) have multiple alignments (1 have >20)

94.7% overall read mapping rate.

Aligned pairs: 433356

 of these:    211726 (48.9%) have multiple alignments

                5512 ( 1.3%) are discordant alignments

91.3% concordant pair alignment rate.

how to interpret all these numbers thank you.

rna-seq • 1.2k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by rajeshkumar_vinod30
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