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!
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.
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.
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version 2.3.6
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?
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."