Question: IGV Fasta Error: Uneven Line Lengths
0
gravatar for eds35016
19 days ago by
eds350160
University of Georgia
eds350160 wrote:

I'm trying to import my reference genome into IGV so that I can view an alignment but IGV doesn't seem to like my reference fasta. I'm assuming IGV is upset over the fact that the fasta has line lengths of 100 bp which I know is not the fasta standard but I'm unsure of how to modify it to fit the 80 bp standard that IGV wants. Any help greatly appreciated!

igv genome • 74 views
ADD COMMENTlink written 19 days ago by eds350160

I'm assuming IGV is upset over the fact that the fasta has line lengths of 100 bp which I know is not the fasta standard

There is NO fasta standard.

https://twitter.com/tim_yates/status/559103153636143104

ADD REPLYlink modified 19 days ago by RamRS25k • written 19 days ago by Pierre Lindenbaum124k

Ah I see. I was going off of information I found here but would the 100 bp line length is the issue or is this something IGV natively supports?

ADD REPLYlink written 19 days ago by eds350160

igv uses htsjdk , and there is no restriction on length. https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/samtools/reference/FastaSequenceIndexCreator.java#L105

ADD REPLYlink written 19 days ago by Pierre Lindenbaum124k

There is no restriction length however, all the sequences have to be the same length.

ADD REPLYlink written 18 days ago by swbarnes27.0k
0
gravatar for Pierre Lindenbaum
19 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

are you able to index the reference with

samtools faidx  your.fa

? = do all your fasta lines have the same length ?

ADD COMMENTlink written 19 days ago by Pierre Lindenbaum124k

After checking, it turns out there are lines of varying length after all. Is there any way to compress each of the contigs into one large line and then split them evenly from there?

ADD REPLYlink modified 19 days ago • written 19 days ago by eds350160

NormalizeFasta (Picard) https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.7.0/picard_reference_NormalizeFasta.php

Normalizes lines of sequence in a FASTA file to be of the same length.This tool takes any FASTA-formatted file and reformats the sequence to ensure that all of the sequence record lines are of the same length (with the exception of the last line).

https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.7.0/picard_reference_NormalizeFasta.php

ADD REPLYlink written 19 days ago by Pierre Lindenbaum124k
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