Welcome to Biostar!
Add New Post
How does bwa perform soft-clipping?
4.2 years ago by
Given a read, how many bases does bwa determine to be soft-clipped from the beginning?
• 1.4k views
Follow via messages
Follow via email
Do not follow
4.2 years ago
to add an answer.
Similar posts •
How does picard CollectWGSmetrics estimate coverage on Soft-Clipped Reads?
Does picard CollectWGSMetrics take into account soft-clipped reads to estimate mean coverage? Ali...
How is mate alignment which may generate soft-clipping signature implemented in bwa?
Would one please describe the mate alignment algorithm that has been implemented in bwa? Is it ki...
Why Is Bwa Soft-Clipping Exactly Matching Reads?
I am using bwasw to align reads from a MiSeq run to a very short reference sequence. For some rea...
How to extract forward and reverse primer coordinates for soft clipping?
Hello, I have a list of forward and reverse primers for ~400 amplicons and I want to extract the...
Soft-clipping of reads in Amplicon-sequenced data
I have a variant calling pipeline which I use to process amplicon-sequenced fastq files; it uses ...
bwa mem hard clipping
Hi all, I apologize if this question has been posted or answered earlier. But I did not seem to...
Difference between Hard Clip and Soft Clip in Samtools CIGAR string
Hi all, The documentation for Samtools is minimal at best. I'm still confused on the concept of...
Add soft clipping to a bam file
Hi, does anyone have a way of adding soft clipping to a bam file? I want to see what happens if ...
No soft-clipping in BWA 0.7.10 anymore?
Hi all! After moving from bwa version 0.5.8c to 0.7.10 I discovered differences that look like e...
Soft-Clipping And Variant Calling
Having aligned my reads with BWA-mem, I noticed that a lot of alignments are dodgy, to put it mil...
Soft-Clipped Vs Unmapped?
quite confused about this two terminology. I'm reading Pindel, the split-read algorithm. The auth...
How to extract coordinate of hard and soft clipped long reads ?
I wanted to extract the genome coordinate of all those location where longreads are soft/hard cli...
I have short reads that end in a non-genomic sequence. Clipping the reads before mapping is possi...
Bwa/Samtools Soft-Clipping To Retrieve Back Whole Read
Hi, (I've been googling for this and couldn't find the answer) Am I right in thinking that the ...
How can I split the soft clipped reads and map the splitted reads again.
I have a question regarding unmapped reads. From SRBreak paper: "If reads are aligned across brea...
Disable Soft-Clipping Bwa Aln
Is there a way to tell bwa aln to do not soft-clip reads and try to align them? We see that man...
Remove Soft Clipped Bases
I want to conduct some computations using a python script directly on some BWA aligned bam files,...
Extract soft-clipped reads from BWA -generated SAM file
Hi, I aligned Illumina-generated, paired-end reads to reference sequence using bwa-mem. Now, I w...
Double soft-clipped reads and how to romeve them
Hi I have some reads aligned with bwa 0.7.15, and I've found some regions with reads ending with...
Is there any aligner which supports soft clipping a fixed number of bases from reads prior to alignment?
I'm working on a project where the read data consists of 6-mers ligated to the 5' end of a sequen...
Use of this site constitutes acceptance of our
Traffic: 884 users visited in the last hour