Definiton Of Singletons

Hi all,

I wonder if anyone would care to tell me what is the official definition of reads falling in the "SINGLETONS" category according to Flagstat (in paired end sequencing)

Thank you in advance for your kindness! gio

alignment samtools

• 2,211 views • link

updated 12.8 years ago by Sam

• written 12.8 years ago by mujupas

1 answer

You can find a relevant discussion here

Basically, it should be reads that only one of the pairs are aligned to the genome

• 225 views • link

written 12.8 years ago by Sam

Mmm thanks but why the "should be"? Isn't there an official agreement about this? It's actually surprising that it's not so easy to retrieve this information...

• 0 views • link

written 12.8 years ago by mujupas

More posts like this

"Secondary", "Supplementary", "Duplicates" and "Paired in sequencing" in samtools flagstat
written 4.4 years ago by pasha64t •

I wonder if someone please explain what secondary, supplementary, duplicates and paired in sequencing mean in samtools flagstat Example: ``` 194492 + 0 in total …
How to remove singletons in a BAM file using samtools
written 7.7 years ago by neranjan •

Dear All, I want to remove the singletons from the aligned bam file. Downloaded fastq files using fastq-dump --split-files SRR1517848 Then aligned the paired end …
Counting paired-end sequencing mapped reads
written 9.2 years ago by heir_of_isildur88 •

Hi all, I have a very basic question here. With a paired-end sequencing, how do we count the number of mapped reads? I did a …
Flagstat results: 0 reads
written 10.1 years ago by rmande •

Hi, I ran samtools flagstat on a bam file I aligned from paired end fastqs using bwa-mem and this is the result I got. 141275694 …
samtools flagstat result is different from samtools view result
written 10.4 years ago by Louis Kok •

Hi All. I wonder if anyone of you have inconsistent mapping result generated by `samtools flagstat` and `samtools view` command? My samtools flagstat output is …
QC based on Samtools Flagstat
written 12.1 years ago by indranipoddar •

Hello, It will be very helpful if somebody can please suggest me if the this a poor alignment or not and I need to exclude …
How To Cluster Mate Pair, Paie End And Single End Reads From Single File??
written 12.7 years ago by HG

Hi, I made mate pair illumina sequencing. In fastq file i checked mate pair, paie end and single end reads are present. Can any one …
Getting Confused With The Flagstat After Pcr Duplicates Removed
written 14.3 years ago by KJ Lim •

Good day. I encountered a situation like below: The flagstat before PCR duplicates removed from paired end mapped reads. <pre><code>:::::::::::::: 0H.flagstat.txt :::::::::::::: …
What Does Qc-Passed/Failed Reads Mean In Samtools Flagstat?
written 14.6 years ago by KJ Lim •

<pre><code>8075928 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 4723128 + 0 mapped (58.48%:nan%) 8075928 + 0 paired in sequencing …
Samtools Flagstat Output
written 14.7 years ago by Nitram •

For past two hours I tried to browse around for samtools flagstat output information, unfortunately could not find much related to my problem - this …