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2 hours ago by

Morocco

Hello Biostar
I hope you're doing well
i mapped my reads against the reference genome to get an idea about the coverage , what i want to know is the percentage of the coverage , but i don't know how to obtain this information using the diffrent tools i know , in qualimap , i just found the mean coverage and std coverage data also lines like this

There is a 99.59% of reference with a coverageData >= 1X
     There is a 99.56% of reference with a coverageData >= 2X
     There is a 99.53% of reference with a coverageData >= 3X
     There is a 99.49% of reference with a coverageData >= 4X
     There is a 99.45% of reference with a coverageData >= 5X
     There is a 99.42% of reference with a coverageData >= 6X
     There is a 99.39% of reference with a coverageData >= 7X
     There is a 99.37% of reference with a coverageData >= 8X
     There is a 99.34% of reference with a coverageData >= 9X
     There is a 99.31% of reference with a coverageData >= 10X
     There is a 99.3% of reference with a coverageData >= 11X
     There is a 99.27% of reference with a coverageData >= 12X

..

i don't know if it s possible to obtain the percentage of the coverage using this informations and how ,
Also i used bamtools stats , and obtained these informations

Total reads:       6158542
Mapped reads:      5749217  (93.3535%)
Forward strand:    3286294  (53.3616%)
Reverse strand:    2872248  (46.6384%)
Failed QC:         0    (0%)
Duplicates:        0    (0%)
Paired-end reads:  6158542  (100%)
'Proper-pairs':    4667096  (75.7825%)
Both pairs mapped: 5730384  (93.0477%)
Read 1:            3079271
Read 2:            3079271
Singletons:        18833    (0.305803%)

and the same thing i didn't get the percentage of coverage
and the same thing with samtools flagstat

6158542 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
5749217 + 0 mapped (93.35% : N/A)
6158542 + 0 paired in sequencing
3079271 + 0 read1
3079271 + 0 read2
4667096 + 0 properly paired (75.78% : N/A)
5730384 + 0 with itself and mate mapped
18833 + 0 singletons (0.31% : N/A)
83794 + 0 with mate mapped to a different chr
12721 + 0 with mate mapped to a different chr (mapQ>=

5)

and samtools idxstatsNZ_

ALWU01000001.1  581415  2031429 6451
    NZ_ALWU01000002.1   43553   76489   678
    NZ_ALWU01000003.1   29286   117672  342
    NZ_ALWU01000004.1   37537   144448  440
    NZ_ALWU01000005.1   217837  789901  2467
    NZ_ALWU01000006.1   38235   103338  325
    NZ_ALWU01000007.1   9944    45471   292
    NZ_ALWU01000008.1   178611  651422  2190
    NZ_ALWU01000009.1   17047   6352    42
    NZ_ALWU01000010.1   510276  1782695 5606
    *   0   0   390492

can you tell me please how to get the percentage of the coverage ?
Thank you very much



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