How to get information (Count) of Unique Mapped Reads to the Genome?
Hi,
I would like to check how many reads are uniquely aligned or mapped to the Genome (or Chromosomes)? I had aligned my data using the BWA aligner.
Would be grateful If I could get suggestions regarding this query.
I know that there is a command to check information about multi-mapped reads. If I am not mistaken.
samtools view -c fixed.bam
Thank you so much in advance.
• 1,925 views
•
link
written
by
ramshahaya •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Why Is My Uniquely Mapped Read Count Higher in Samtools Compared to Bowtie2?
written by daffodil •
-
Uniquely mapped paired-end reads on the same chromosome
written by barzilayrom1 •
-
Haplotype Caller GATK Query
written by ramshahaya •
-
not primary alignment flag filtering does not work
written by buffealo •
-
RNA_Seq data aligned used uniquely or multi mapped reads impact on result interpretation
written by Diango •
-
Counting uniquely mapped reads - ambiguous results
written by mickey_95 •
-
difference between mapq=0 and samtools flag 0x900
written by bitpir
-
samtools counting unique mapped reads
written by bitpir
-
Is correct finding unique reads with the flag -F 0x104?
written by miquinhap •
-
How To Get The Correct Alignment Statistics After Using Bwa Mem With -M Option
written by skm770 •
samtools flagstats
samtools flagstats fixed_Sort_Coordinate.bam
9307234 + 0 in total (QC-passed reads + QC-failed reads)
9256458 + 0 primary
50776 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
9255274 + 0 mapped (99.44% : N/A)
9204498 + 0 primary mapped (99.44% : N/A)
9256458 + 0 paired in sequencing
4628229 + 0 read1
4628229 + 0 read2
9056900 + 0 properly paired (97.84% : N/A)
9164336 + 0 with itself and mate mapped
40162 + 0 singletons (0.43% : N/A)
79236 + 0 with mate mapped to a different chr
46085 + 0 with mate mapped to a different chr (mapQ>=5)
Thank you so much for the reply. Which row should I consider in the above results?
Is it possible to check how many uniquely mapped read on different chromosome? samtools idxstats will work? I know, samtools idxstats will provide information about mapped reads on the chromosome. If I am not mistaken. But I would like to see uniquely mapped read on a different chromosomes.
Thank you so much in advance.
Isn't it simply like that: unique = mapped - secondary?
Edit: Sorry, just consulted the documentation. Primary mapped should be a unique count.
So the read is mapped (4 not set), and no secondary or other mapping exist and assuming BWA only gives a single alignment per read.
Thanks a lot