Question: (Closed) Larger number of reads are aligned than input reads
gravatar for SSK
13 months ago by
SSK10 wrote:


I filtered my row reads by Trimmomatic, and aligned those by bwa mem. After that, I count input reads number with 'echo $(gzcat filtered_paird_fastq.gz | wc -l)/4|bc', and sum of the answers was ' 2736865184' .

Also, I count aligned reads number by using ' samtools flagstat bam'. The answer was like below.

2737435510 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 4886994 + 0 supplementary 0 + 0 duplicates 2737435510 + 0 mapped (100.00% : N/A) 2730564232 + 0 paired in sequencing 1365282116 + 0 read1 1365282116 + 0 read2 2270271490 + 0 properly paired (83.14% : N/A) 2730564232 + 0 with itself and mate mapped 0 + 0 singletons (0.00% : N/A) 194256760 + 0 with mate mapped to a different chr 47051705 + 0 with mate mapped to a different chr (mapQ>=5)

I found from this result that QC-passed reads ( line 1 ) is larger than input reads.

So, I want to ask what is the cause of this?


bwa fastq alignment ngs • 322 views
ADD COMMENTlink modified 13 months ago by Rashedul Islam380 • written 13 months ago by SSK10

Hello SSK!

We believe that this post does not fit the main topic of this site.

Same question duplicated

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD REPLYlink written 13 months ago by SSK10
gravatar for Rashedul Islam
13 months ago by
Rashedul Islam380 wrote:

Same question duplicated here.

ADD COMMENTlink written 13 months ago by Rashedul Islam380
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