Hello everyone,
First of all, I know there has been a lot of discussions related to uniquely mapped reads estimation (sorry for bringing...
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Can the "QNAME" information of a SAM file be used for estimate uniquely mapped reads?
Last edited by znasim09; 08-02-2018, 07:09 PM. -
Yet Another bwa mem unique post
So, I am using the following version of BWA
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.12-r1039</pre>... -
HELP!! XS tag to filter unique reads Do NOT match bowtie2 report
I find the XS tag filtering the uniquely mapped reads number is different from the bowtie2 report. I first extract the flag number of 147/99 + 163/83... -
BWA XT:A:U and XA for same read?
Apologies if this has been asked before, but I can't see an answer and can't seem to figure this out.
Looking at the BWA documentation... -
Filtering uniuque reads from a bam file
Hello everyone,
I created a bam file with tophat:
...Code:tophat2 --color --quals -x 1 --library-type fr-secondstrand --read-realign-edit-dist
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Bowtie: How to retain only uniquely mapped reads?
Hi!
I have been searching for the answer to this questions on the internet (google, this forum, bowtie manual), but can't find a clear... -
bowtie -m option
Hi everybody,
maybe I misunderstood it completely, but what is the option -m good for?
If I am looking for differentially regulated... -
Regarding Unique reads, Unique alignments
I have few questions regarding the best practices that are adopted, in dealing with multiple alignments from a single read and presence of identical reads... -
Aligning only unique reads in Bowtie
Hi everyone,
I am aligning some ChIP-seq data using Bowtie. I have been using the -m option to throw out any reads with > 1 reportable...
