Question: loaded a sorted bam file in IGV but I can't see anything
0
gravatar for saadleeshehreen
5 months ago by
saadleeshehreen60 wrote:

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.

igv bam assembly • 351 views
ADD COMMENTlink modified 5 months ago by Emily_Ensembl17k • written 5 months ago by saadleeshehreen60

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

ADD REPLYlink written 5 months ago by finswimmer11k

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

Untitled

ADD REPLYlink modified 5 months ago • written 5 months ago by saadleeshehreen60

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

ADD REPLYlink written 5 months ago by finswimmer11k

Zoom in to the maximum perhaps

ADD REPLYlink written 5 months ago by rse70

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?

Untitled_2

ADD REPLYlink written 5 months ago by saadleeshehreen60
1
gravatar for arup
5 months ago by
arup870
India
arup870 wrote:

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

ADD COMMENTlink written 5 months ago by arup870

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

ADD REPLYlink written 5 months ago by Titus770
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