11 results in 0.0030 seconds.
-
samtools v1.7 flagstat tsv output formats
I'm using samtools v1.7 flagstat command to summarize a reference alignment I've performed using paired-end data. I understand the output alright (attached),... -
Incosistent number of paired end reads (BAM file generated by STAR using RSEM)
I have used RSEM to quantify paired-end RNA-Seq data. The alignment was done
using STAR which was called internally by RSEM, using a reference... -
hisat2 output more reads than are in the file
Hi all,
I am in the middle of testing the hisat2 mapper and encountered a discrepancy between the output hisat2 gives me at the end of the mapping... -
flagstat/ht-seq discrepancy
Hello,
I am trying to understand a discrepancy between alignment numbers reported by flagstat and ht-seq. I have a BAM file from tophat2 which... -
Uniquely mapped reads from BAM file (BWA)
Hi all,
I know this question has been asked many times. But, I am still not able to find the proper answer. So, how do you caluclate the... -
Flagstat vs. Picard AlignmentSummaryMetrics
Hi everyone,
I am having a bit of trouble making ends meet with this two tools.
I have a whole genome realigned with GATK and am trying... -
Samtools flagstat 0% properly paired
Hi,
I have used BWA 0.75a to map PE data of WGS to reference, and samtools flagstat to check the resulting BAM file. My pipeline includes... -
Samtools flagstat
Hi there,
I ran tophat a few months ago on our rna-seq dataset and made a table showing the mapping statistics from samtools flagstat.... -
samtools & flagstat & awk
Hi,
Here is my command :
$ samtools merge L002_LBCO1.bam L002_LBCO1_chr*.bam
$ samtools view L002_LBCO1.bam | awk '$3==... -
SAMtools flagstat output interpretation
Hi,
I got the following info after running a samtools flagstat on a Novoalign bam file:
126597089 in total
0 QC failure... -
bam to sam coversion and flagstat
Hi Everybody,
I converted the Tophat result accepted_hits.bam to .sam using
samtools view accepted_hits.bam > accepted_hits.sam...
