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Old 03-02-2017, 02:29 AM   #1
pkseq2017
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Default Problem loading refFlat file into IGV

Hello All,


While trying to load a refFlat file into IGV, the app warns:

Files must be sorted by start position prior to indexing. Input file is not sorted by start position. ... Note: igvtools can be used to sort the file, select "File > Run igvtools...".

I tried to use igvtools sort command which returns a null error, what is the common method to sort such files otherwise? Or is this covering another problem with the file?


Thank you!
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Old 03-02-2017, 02:35 AM   #2
pkseq2017
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P.S: I am new, not sure if this is the 100% related forum to post this
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Old 03-02-2017, 10:05 AM   #3
Brian Bushnell
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This is absolutely the right forum for problems with bioinformatics software

Can you describe the situation in more detail? I'm not sure what you mean by a "refFlat file".

Normally, when I use IGV, I select from the menu to load a reference genome fasta file, which does not require any sorting. Once that is loaded, I drag and drop a bam file into the window. The bam file consists of mapped reads and must be sorted by position, and indexed. The reads must have been mapped to the exact fasta file you loaded into IGV as the reference.

So, please provide some additional details about what you're doing.
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Old 03-03-2017, 07:18 AM   #4
pkseq2017
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Hi! Thank you

refflat is the extension for a special kind of gene annotation file.
Seems that IGV supports this file type "if" it is sorted and indexed already.
So I tried pysam and samtools (well the same), but they are also not able to sort this file type.
That's why, now I am looking for an application which actually supports this poor refflat fully...
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