loaded a sorted bam file in IGV but I can't see anything

Question

[saadleeshehreen]

Hi,

I have genomic SRR file (DNA-seq) for a pseudomonas genome. I used a file containing corresponding cDNA sequence and nucleotide sequence of my gene of interest to build the index by using the salmon tool. Then, used samtools to create SRR.bam file

salmon quant -p 10 -i  SRR_index -l A -1 SRR_1 .fastq -2 SRR_2.fastq -z -o SRR_qt | samtools view -bs > SRR.bam
samtools sort SRR.bam SRR.sorted.bam
samtools index SRR.sorted.bam

Then load the .fasta files ( the index.fasta.fai was in the same directory), *.gff files of the to the IGV. I also loaded .sorted.bam file in IGV but I can't see anything.

Please give me a solution.

[finswimmer]

Hello,

but I can't see anything

A screenshot would be useful to understand what you see and what not. Try to zoom in, as IGV doesn't show a coverage track or read information if the region of the current view is to large.

fin swimmer

[saadleeshehreen]

Red box is the region I want to see. The file is quite different from the tutorial page. Shouldn't I saw grey bars for bam files? https://wikis.utexas.edu/display/bioiteam/Integrative+Genomics+Viewer+%28IGV%29+tutorial

My intention was to understand the piece come from any integrated elements or not. The genomic data ( as its contig level assembly) didn't give me the clear indication

[finswimmer]

Hello again,

there would be grey bars (those would be the aligned reads) if you:

1. have a valid alignment file
2. zoom in enough

I don't know salmon. But after a quick look at the manual it doesn't look like the output is an alignment file, isn't it? I guess you have to choose this before with another program like bwa or bbmapor ...

fin swimmer

[rse]

Zoom in to the maximum perhaps

[saadleeshehreen]

Thanks. I use BWA and now the alignment look like that.. I didn't split the window. But I get two alignment near the position of my gene of interest. What does it mean?

Answer 1

[Arup Ghosh]

Salmon is a pseudoaligner so clearly, the output you are getting does not have mapping information. Try --writeMappings argument to include the alignment information.

Ref: https://salmon.readthedocs.io/en/latest/salmon.html

[Titus]

To add information , i never be able to read the BAM (convert from the SAM output ) with IGV with this option.