Entering edit mode
6.6 years ago
jerryyyyy
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0
We have our first genome data loaded on our computer (good news) and trying to read it using some of the standard tools but we are getting some errors.
We are using NCBI Genome Workbench. When we try to read in ch11, we get an error.
“graphical view failed to retrieve sequence for id lcl”
There has been a post here about this and it appears that the bai associated with our BAM file may need to have a standard reference?
Not sure how we get that. The WGS was done by Macrogen.
We can load the test data with no problem.
We get a similar fail to read with java-based IGV software, so I think it is a file compatibility issue.
Thanks for your help!
suggestion; try to re-index the BAM file using https://software.broadinstitute.org/software/igv/igvtools_gui (see "Index" ). Show us any error message.
lcl is a prefix used by NCBI to prefix the local accession numbers. ( https://www.ncbi.nlm.nih.gov/books/NBK279675/ ). if the fasta sequence name is, in the end: "lcl 12345", the indexers (like samtools faidx) , will just read 'lcl'
Sorry, I truncated the error message. It was actually "Graphical view: failed to retrieve sequence for id lcl|chr11". Think the error must be elsewhere.
yes, try to re-index with IGV-tools