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

ADD COMMENTlink 16 months ago saadleeshehreen • 60 • updated 16 months ago Emily_Ensembl 18k
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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 16 months ago
finswimmer
11k
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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 16 months ago
saadleeshehreen
• 60
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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 16 months ago
finswimmer
11k
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Zoom in to the maximum perhaps

ADD REPLYlink 16 months ago
rse
• 90
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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 16 months ago
saadleeshehreen
• 60
1
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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 16 months ago arup ♦ 1.3k
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To add information , i never be able to read the BAM (convert from the SAM output ) with IGV with this option.

ADD REPLYlink 16 months ago
Titus
• 850

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