Question: why Samtools Flagstat Results showing very less reads mapped
0
gravatar for inayat45shaikh
5.4 years ago by
India
inayat45shaikh40 wrote:

Hello group,

i am trying to get the percentage of reads mapped to refernce using samtools. i used the command samtools flagstat sequence.bam , but the result i am getting is bit worst than i was expecting, as it shows only 34% of reads mapped.

438974667 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
151842378 + 0 mapped (34.59%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

i wanted to know why i am getting this result, and where have i done mistake and how can fix this problem.

Thanks in advance

 

next-gen • 1.7k views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 5.4 years ago by inayat45shaikh40
1

I need to know more to be able to answer that -

What program did you use for alignments? Which settings, what insert size did you use? How complete is your reference? Is it the same species, or are you using a different reference genome? Is it mate-paired data? Did you have a look at the quality of your reads using FastQC?

 

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Philipp Bayer6.5k

Hi Philipp,

i have a single-end data and i want to map this to its assembled contigs to assess assembly quality and calling variants. i used BWA for alignment.

ADD REPLYlink written 5.4 years ago by inayat45shaikh40
1

How well reads will map to assembled contigs will depend entirely on the quality of the assembly. My guess is that this assembly is a bit lacking.

ADD REPLYlink written 5.4 years ago by Devon Ryan92k
1
gravatar for Devon Ryan
5.4 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

The results that it shows are simply the metrics that exist. If you want a higher alignment rate, then perhaps tweaking the aligner settings or changing how reads are pre-processed would be useful. Samtools just reports what's in the BAM file, nothing more.

ADD COMMENTlink written 5.4 years ago by Devon Ryan92k
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