Follow up: using zip files af refseq

[MehdiiYac]

Hello i tried using zipped files as refseq and got the following display

For information here is my tracks.conf file:
[GENERAL]

highResolutionMode=auto

refSeqs=iwgsc_refseqv2.1_assembly.fa.fai

[tracks.IWGSC_RefSeq2_1]

urlTemplate=iwgsc_refseqv2.1_assembly.fa.gz

storeClass=JBrowse/Store/SeqFeature/IndexedFasta

type=Sequence

category=Reference Sequence

description = IWGSC RefSeq v2.1

Did i do something wrong?

Thanks and sorry for asking so many questions

[cmdcolin]

I think you can fix it with storeClass=JBrowse/Store/SeqFeature/BgzipIndexedFasta

no worries :)

[MehdiiYac]

Hello, i tried that but the sequence keeps loading forever:

Do you have any idea of what could be wrong?

[MehdiiYac]

@cmdcolin (just in case you didn't see it)

[cmdcolin]

@MehdiiYac not exactly sure, thanks for the reminder though. I created a test case where I loaded a genome using a config that looks like yours and it worked ok. here is a config that works for me

[GENERAL]
highResolutionMode=auto
refSeqs=iwgsc_refseqv2.1_assembly.fa.gz.fai
[tracks.IWGSC_RefSeq2_1]
urlTemplate=iwgsc_refseqv2.1_assembly.fa.gz
storeClass=JBrowse/Store/SeqFeature/BgzipIndexedFasta
type=Sequence
category=Reference Sequence
description = IWGSC RefSeq v2.1

note that i use .gz.fai not just .fai. you should run samtools faidx on the bgzip fasta e.g. samtools faidx file.fa.gz