Question: Do I need to provide the Illumina's target region bed file for qualimap?
0
gravatar for bioinforesearchquestions
3.2 years ago by
United States
bioinforesearchquestions280 wrote:

Hi friends,

I have trio exome sequencing data with me. In order to know the coverage for trio samples. I used qualimap tool. Why is the mean coverage very low only 5.3X. Generally, exome sequencing have 80-100X coverage right. I didn't provide the reference file for the tool. Do I need to provide the Illumina's target region bed file?

  • This is the command I used

qualimap bamqc -bam sample1.bam -nt 8 sample1.bamqc -outformat PDF --java-mem-size=4G

  • Output:

Reference size: 3,137,161,264 bp

Number of contigs: 93

Number of reads: 131,279,965

Mapped reads: 131,082,678 (99.85%)

Unmapped reads: 197,287 (0.15%)

Duplication rate: 57.68%

Mean Insert size: 188

Chrom_Cov

Chromosome stats:

Chromosome_Stats

ADD COMMENTlink modified 3.0 years ago by Raony Guimarães1.1k • written 3.2 years ago by bioinforesearchquestions280
2
gravatar for igor
3.0 years ago by
igor12k
United States
igor12k wrote:

You didn't give it a list of targets, so it calculated genome-wide coverage. From the SD, you can see that there are some regions that have much higher coverage.

How can it calculate on-target coverage if you don't give it the targets?

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by igor12k
0
gravatar for trausch
3.0 years ago by
trausch1.5k
Germany
trausch1.5k wrote:

I don't have any experience with qualimap but the on-target rate and the targeted sequencing coverage can also be computed by Alfred (disclaimer: my own tool).

ADD COMMENTlink written 3.0 years ago by trausch1.5k
0
gravatar for Raony Guimarães
3.0 years ago by
Dublin / Ireland
Raony Guimarães1.1k wrote:

You need to provide a bed file with the target regions specific to your exome target kit or you can use a generic with the official list of exome regions from UCSC.

ADD COMMENTlink written 3.0 years ago by Raony Guimarães1.1k

It depends on your question. If you want to know how well the capture worked, then you should use the regions that are designed to be captured. If you want to see if specific genes are captured, then you should use a BED file for those genes (just be careful to not include introns).

ADD REPLYlink written 3.0 years ago by igor12k

Hi guys,

I have a query, if I have a low-pass sequenced whole genome data. Should I need to give UCSC bed file or no need of it?

I downloaded the exome interval file from the sequencing kit website. After using the exome interval file, the mean coverage is 224X.

">>>>>>>" Coverage

 mean coverageData = 224.4677X
 std coverageData = 328.406X

 There is a 99.6% of reference with a coverageData >= 1X
 There is a 99.47% of reference with a coverageData >= 2X
 There is a 99.21% of reference with a coverageData >= 3X
 There is a 99.04% of reference with a coverageData >= 4X
 There is a 98.8% of reference with a coverageData >= 5X
 There is a 98.61% of reference with a coverageData >= 6X
 There is a 98.36% of reference with a coverageData >= 7X
 There is a 98.14% of reference with a coverageData >= 8X
 There is a 97.9% of reference with a coverageData >= 9X
 There is a 97.67% of reference with a coverageData >= 10X
 There is a 97.41% of reference with a coverageData >= 11X
 There is a 97.17% of reference with a coverageData >= 12X
 There is a 96.91% of reference with a coverageData >= 13X
 There is a 96.67% of reference with a coverageData >= 14X
 There is a 96.4% of reference with a coverageData >= 15X
 There is a 96.14% of reference with a coverageData >= 16X
ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by bioinforesearchquestions280
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