Index file making for Triticum aestivum

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4.3 years ago

shokrabad ▴ 10

Hello everybody. I want to align my rnaseq files to the reference genome of wheat using HISAT2. We need index file in it's procedure. My question is: Is there any index file for Triticum aestivum to ddownlad? Probably no. So my main question is how much memory (RAM) do I need to build that? My reference genome size is almost 17 giga base. Thank you.

RNA-Seq HISAT Index file • 1.4k views

ADD COMMENT • link updated 2.1 years ago by Laila • 0 • written 4.3 years ago by shokrabad ▴ 10

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Probably difficult to predict accurately but you may need close to 100G of free RAM for the index creation.

ADD REPLY • link 4.3 years ago by GenoMax 141k

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See if this helps you:

ftp://ftp.ensemblgenomes.org/pub/plants/release-45/fasta/triticum_aestivum/dna_index/

ADD REPLY • link 4.3 years ago by cpad0112 21k

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@cpad112 that index can't be used with NGS alingers. That is just an indexed fasta file.

ADD REPLY • link 4.3 years ago by GenoMax 141k

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@ genomax : I realized later. Thanks

@ shokrabad : I was able to index using 32 gb RAM, core i7 machine using BWA. It took many hours via CLI. With bowtie it failed (didn't complete on galaxy). I downloaded the sequence from IWGSC (URGI).

ADD REPLY • link 4.3 years ago by cpad0112 21k

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Thanks. I'm going to run using a server with 128gb RAM, 24 core. Then I'll report the result here soon.