Question: i want to upload a single indexed fasta file containing many viruses genome to the IGV
0
gravatar for Dr. Tahir Usman
3.4 years ago by
Rostock, germany
Dr. Tahir Usman0 wrote:

I have created a single fasta file of the many viruses gennome. I have indexed the fasta file and also the bam file. Now i want to upload the indexed fasta file into the IGV. Doing so, the IGV give an error "Contig 'gi|168480155|ref|NC_010354.1|' already exists in fasta index." How to fix this problem. Please help!

rna-seq • 1.1k views
ADD COMMENTlink modified 3.4 years ago by geek_y9.8k • written 3.4 years ago by Dr. Tahir Usman0

If you are trying to upload this to use as a custom genome you should select the original fasta file (not the index file). Is that what you are trying?

ADD REPLYlink written 3.4 years ago by genomax69k

I want to view the indexed bam files the indexed pathogen (viruses and bacteria genomes) fasta files in IGV for allignment. and while uploading the indexed fasta files i found this error "Contig 'gi|168480155|ref|NC_010354.1|' already exists in fasta index."

ADD REPLYlink written 3.4 years ago by Dr. Tahir Usman0
0
gravatar for geek_y
3.4 years ago by
geek_y9.8k
Barcelona
geek_y9.8k wrote:

What is the output of

grep "^>" in.fasta | sort | uniq -c |  sort -k1,1nr | head

Its most likely because of duplicate fasta headers i.e duplicate names in fasta sequences.

ADD COMMENTlink written 3.4 years ago by geek_y9.8k

Thanks Goutham Atla, yeah, perhaps that could be a reason. How can i fix it?

ADD REPLYlink written 3.4 years ago by Dr. Tahir Usman0

If there are duplicate entires in the fasta file, you can remove them using some command as below:

grep "^>" in.fasta | sed 's/^>//g' | sort | uniq > uniq_ids.txt
samtools faidx in.fasta `cat uniq_ids.txt ` > new.fasta
samtools faidx new.fasta

. But if there are duplicate headers but not duplicate sequences, its a bit tricky as you have already aligned the data.

ADD REPLYlink written 3.4 years ago by geek_y9.8k
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