Parse mapped scaffolds in BWA alignment

Hi all,

I'm learning bioinformatics from scratch, please bear with me, if I go wrong.

I sequenced (miseq) few of my BACs. I mapped these miseq reads on reference genome using BWA. My question is, how to parse out names of the scaffolds of my reference genome got mapped from alignment file?

Many Thanks

sam ngs bwa bam

• 2,962 views • link

updated 4.1 years ago by Ram

• written 11.3 years ago by second_exon

1 answer

Here is SAM file format specification. You need to use samtools to view the contents of sam/bam file and then manipulate.

If you want to see the scaffolds:

samtools view <input bam> | cut -f3 | less

• 0 views • link

updated 4.1 years ago by Ram

• written 11.3 years ago by GouthamAtla

Thank you! It worked!!

• 0 views • link

written 11.3 years ago by second_exon

More posts like this

Mapping an assembled genome to a sex chromosome
written 4.8 years ago by Lilnet •

Hi, I would like to find out if there is a method to determine which scaffold were successfully mapped to the reference. In my case …
Alignment of targeted sequencing to the whole genome or to targeted reference
written 7.6 years ago by biobiu

I've sequenced targeted DNA panel. I'm aligning it using bwa mem once to the whole genome and twice to the targeted sequences. When aligning it …
Filter sam/bam files
written 8.1 years ago by second_exon

Hi: I mapped single-end sequenced GBS reads onto two similar genomes. I have two sam files one for each genome. I'm interested to filter sam/bam …
Mapping scaffolds to another reference genome
written 9.6 years ago by ash.t.cook •

Hello, I have mapped RAD-PE reads to a reference genome (that consists only of scaffolds without the assignment of scaffolds to any chromosome) and called …
How to call heterozygous SNPs
written 9.7 years ago by second_exon

We sequenced and assembled a genome. Now, I'm interested to call all heterozygous SNPs of the same genome. For that, I mapped paired end reads …
subsetting sets of scaffolds based on sequence similarity
written 11.3 years ago by second_exon

Hi, Couple of months back, I sequenced (MiSeq) few BACs and assembled (Paired-end reads) using SOAPdenovo, but my assembly was fallen into many scaffolds. Now, …
Better statergy for Gap Closing
written 11.3 years ago by second_exon

Hi Guys, Couple of months back, I sequenced (MiSeq) few BACs and assembled (Paired-end reads) using SOAPdenovo, but my assembly was fallen into many scaffolds. …
Patchy alignment in bowtie
written 11.6 years ago by second_exon

I am biologist, learning bioinformatics, please bear with me, if I go wrong in basics. I assembled mi-seq reads ranging between 33-340bp using velvet. I …
BAC sequencing issues
written 11.7 years ago by int11ap1

Hello, I have paired-end Illumina reads from several BACs of an unsequenced plant species. After assembling them using SOAPdenovo, I realized the total assembled size …
Is It Possible To Align A New Sequence With An Existing Maf Multiple Alignment?
written 13.4 years ago by Ryan Thompson

<p>I am trying to annotate the genome of a recently-sequenced primate species. I noticed that the UCSC browser folks have performed a 46-species whole-genome multiple …