ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR358/ERR3580717/scrEXT030_hg19_S11_L001.bam
ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR358/ERR3580718/scrEXT030_hg19_S11_L002.bam
ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR358/ERR3580719/scrEXT030_hg19_S11_L003.bam
ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR358/ERR3580720/scrEXT030_hg19_S11_L004.bam
ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR358/ERR3580721/scrEXT030_hg19_S11_L005.bam
ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR358/ERR3580722/scrEXT030_hg19_S11_L006.bam
For those bam files, samtools output all reads as unmapped. When I checked the bam files, I found the flag in all reads were 4.
samtools view -f 4 scrEXT030_hg19_S15_L002.bam | cut -f1 > S15_L002_unmapped_reads.txt
Why all those reads in bam files were unmapped?
2 answers
The reads are probably in uBAM (Unmapped BAM) file format. It is a way to store raw reads that is sometimes preferred to fastq as it allows you to attach metadata to the reads.
My aim is to extract the unmapped reads without the host sequence. Now there is no way to extract the unmapped reads from uBAM is there? I can only transform these uBAMs into fastq and then use bowtie2 to remove the host sequences? Could you kindly add a line of samtools fastq code to clarify your point?
Correct. If there are no alignments included (as seems to be the case) then you will need to do alignments yourself to extract the reads. One way to do that would be to bin the reads using bbsplit.sh from BBMap suite (example BBSplit syntax for generating builds for the reference genome and how to call different builds. replace with your genomes).
samtools fastq is described in manual page here.
they should really name them .ubam. calling them .bam only leads to confusion
Could well be unmapped BAM files, so the reads were stored in unaligned BAM format rather than fastq. That is not unusual. You will need to check whether there are some information about the processing of these files available. The hg19 indeed suggests some alignment, but file names are usually poor sources of information.
Log in to answer this question.
-
Purpose and necessity of removing PCR duplicates in m6A-seq analysis
written by remagen •
-
Issues with RAT in CAT_pack and Optimizing Relative Abundance Calculation
written by LuciaNhu •
-
No Unmapped Reads in bam file?
written by erik.burchard •
-
IGSR Read Group Data for Base Quality Score Recalibration
written by angus.gane •
-
Decipering .BAM file from Ion Torrent reads
written by newbio17
-
BAM to fastq with Tophat aligned files
written by frameshift •
-
Tutorial: InsideDNA: Analysing transcription factors with ChIP-Sequencing data: a full bioinformati…
written by shilparaopradeep •
-
Using bowtie2 to create BAM files to view strand-specific coverage in Artemis
written by Chris S.
-
Tutorial: Mapping Reads With Bwa And Bowtie
written by MSU course 2011 •
-
Converting Sam Files To Bam Files - Reproduce Results Nature Paper: Transcriptome Genetics Using Se…
written by Sander Timmer
