Read Counts from BAM file
for a set of samples, paired end nextseq illumina p2 was performed. in all, i am getting read count much higher than my actual flow cell capacity. How is it even possible?
my flow cell can generate total reads upto one billion (paired-end), and i see a total of 12 billion!
this was the command to get total and primary aligned reads. the exact figure i got from Qualimap as well.
samtools view -c sample1.bam
samtools view -c -F 260 sample1.bam
can anyone comment on this...?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Samtools view only showing read2 for PE mapped reads
written by knickknack •
-
Why Is My Uniquely Mapped Read Count Higher in Samtools Compared to Bowtie2?
written by daffodil •
-
samtools index: failed to create index. ([E::hts_idx_push] NO_COOR reads not in a single block )
written by DareDevil
-
Filtering for primary and secondary reads using sam flags (0 properly paired reads in alignment ste…
written by Marcel Glueck •
-
Samtools flagstat
written by rakszewska •
-
Issue with Duplicates reads in Exom Data
written by Ranan Jyoti Sarma
-
Help with Samtools flags to get only primary, unique, non duplicate aligned reads
written by kerem.wainer •
-
Calculating percentage of reads mapped to a reference genome
written by rujiporn.sun •
-
Understanding subsampling with Samtools
written by m98
-
How to obtain insert sequence from paired-end mapping result (SAM/BAM)
written by gundalav
Please do this: How to count fastq reads and then report back to see whether here is really a problem with the sequencing data or just an alignment issue.
Do it on all fastq files from that run, then sum up.