Questions tagged [reads]

Reads are the sequences output by a sequencing machine after the raw signal (e.g. light, electricity) is converted into bases by a basecaller.

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20 votes
12 answers

Random access on a FASTQ file

I would like to select a random record from a large set of n unaligned sequencing reads in log(n) time complexity (big O ...
winni2k's user avatar
  • 2,256
12 votes
2 answers

Difference between BWA-backtrack and BWA-MEM

Many of my colleagues recommend I use BWA-MEM instead of regular old BWA. The problem is I don't understand why and reading the BWA man page doesn't seem to help the matter. What is the difference ...
David Ross's user avatar
5 votes
2 answers

Reads mapped to exonic, intronic and intergenic regions

After the alignment step I checked the rnaseq metrics of all the samples. Among 40 samples three samples show high percentage of reads mapped to intronic regions. What could be the reason? ...
stack_learner's user avatar
4 votes
2 answers

Why are there missing calls in a VCF file from exome sequencing?

My data is a VCF file generated from an exome sequencing variant call pipeline. I'm not very familiar with the sequencing and variant calling process. I noticed that there are some missing genotypes, ...
Yan's user avatar
  • 143
2 votes
3 answers

How to detect mismatch before mapping in RNA-Seq data

In the methods of this paper, the authors say: Reads were then filtered based on quality score in the UMI region. Any read with >1 low-quality base (phred <=10) were discarded. Reads with more ...
gc5's user avatar
  • 1,783
1 vote
2 answers

Extract reads from bam files by their @RG

How could I extract reads from bam files by their read groups @RG ?, I've got one file containing all reads for 5 samples, the SM is appears NONE, So, I want to extract each sample reads by the @RG ...
Maloki's user avatar
  • 11