Bam aligmnet file viewing.

Question

[vishalchanda364]

Hello, I have been working on this bam file to visualize the alignment, and till now I have not achieved any sort of result, can anyone help me with this issue? I am working on metagenomics data, and trying to use samtools for visualizing the (.bam) file. Thanks in advance.

[Devon Ryan]

What have you tried? What sort of visualization are you looking for?

[vishalchanda364]

I have aligned my data with cpn60 database using bowtie2, and want to remove the unmapped sequences for which I have been struggling. I used the samtools view option but understood nothing.

I want to visualize the aligned data.( Human readable.)

[Devon Ryan]

I used the samtools view option but understood nothing.

What does this mean?

I want to visualize the aligned data.( Human readable.)

In what way? You need to say exactly in what way you want to visualize the data, since the word "visualize" has absolutely no meaning by itself. Do you want to just see the entries in text format? Do you want to load the file into IGV? Do you want something else entirely?

[GenoMax]

Contrary to the program option name view it does not allow one to view the data.

You can remove unmapped reads using samtools view following these directions: How To Filter Mapped Reads With Samtools

[benformatics]

I have no idea if it is widely used for microbiome investigations but for most animals people use IGV: https://software.broadinstitute.org/software/igv/

[vishalchanda364]

Thank you so much for the help

Answer 1

[colindaven]

We use the tablet assembler viewer, JBrowse, or IGV to view metagenomic BAM files of reads aligned to a (FASTA) collection of host and sequences. The aligner is here: https://github.com/MHH-RCUG/Wochenende

We are also writing a coverage viewer to generate coverage diagrams and coverage statistics in python, but this is not completed yet. We will post the script and instructions to the same page when complete.

[vishalchanda364]

Thank you so very much for the help.