Question: Creating reference Index using Bowtie2
0
gravatar for cvu
5.3 years ago by
cvu140
India
cvu140 wrote:

Hi all,

I'm trying to create reference index for all  human chromosomes 22+X+Y+M using bowtie2, but its getting stuck after performing some steps.

ADD COMMENTlink modified 4.8 years ago by SP250 • written 5.3 years ago by cvu140
2

You should add other details in order for us to help you. You should tell us what error it is throwing?

ADD REPLYlink written 5.3 years ago by Ashutosh Pandey11k

it's not giving any error, it is getting stuck. i left it running for 24hours on 8GB RAM system, but it stuck.  

ADD REPLYlink written 5.3 years ago by cvu140

There are some per-built indexes are available ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/. but it seems they are for Bowtie not for Bowtie2 as they have extension .ebwt.

so can i use these indexes for Bowtie2 also ?

ADD REPLYlink written 5.3 years ago by cvu140

No, bowtie1 indices won't work for bowtie2.

ADD REPLYlink written 5.3 years ago by Devon Ryan92k
2
gravatar for Devon Ryan
5.3 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

Just download the prebuilt ones from iGenomes. Note that they don't seem to have the most recent human reference (GRCh38). If you really do need that, just stop the current bowtie2-build process and start it again, this is presumably a one-off even.

ADD COMMENTlink written 5.3 years ago by Devon Ryan92k

ya i want GRch38 reference index. 8GB RAM is enough or it needs more RAM?

i already tried it 3 times but it is not working.

ADD REPLYlink written 5.3 years ago by cvu140

I would expect that that's enough, but I don't have anything with that little RAM with which to test.

ADD REPLYlink written 5.3 years ago by Devon Ryan92k

bowtie2-build -f GRch38.fasta ref_index

please check, above command line arguments i am using. please let me know, if its okay or i am missing something ?

ADD REPLYlink written 5.3 years ago by cvu140

You don't need -f, but that shouldn't be causing the problem. The command looks fine.

ADD REPLYlink written 5.3 years ago by Devon Ryan92k

Do you want the UCSC or Ensembl chromosome names? I can just make the indices and put them on google drive or something for you.

ADD REPLYlink written 5.3 years ago by Devon Ryan92k

I want Ensembl chromosome names (GRch38). please do me a favor, if you can. 

thanks a lot Devon Ryan !!

ADD REPLYlink written 5.3 years ago by cvu140
1

Can do. Is the "primary assembly" OK or do you want "top level" (i.e., with all of the patches and alternate haplotypes)?

ADD REPLYlink written 5.3 years ago by Devon Ryan92k

basically, i'm gonna use this index for mapping reads to find SNPs and INDELs. and i've downloaded dbSNP human build 141(vcf file) based on GRch38 assembly.

please give me whichever is better with above mentioned dbSNP version.

i've also changed sequence identifiers in fasta files according to the name given in dbSNP.

so i can provide you the fasta sequences.

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by cvu140
2

Here are the indices for UCSC (since Ensembl isn't yet available):

https://drive.google.com/file/d/0B3r17kL08B7QQWFpOHNQZmNpN2s/edit?usp=sharing
https://drive.google.com/file/d/0B3r17kL08B7QR3RReFoyLXFfVTg/edit?usp=sharing
https://drive.google.com/file/d/0B3r17kL08B7QWE9NY3pWVVBEREk/edit?usp=sharing
https://drive.google.com/file/d/0B3r17kL08B7QY1BESWtuMVp4Y0U/edit?usp=sharing
https://drive.google.com/file/d/0B3r17kL08B7QZlpDLTBwWjJ3Q3M/edit?usp=sharing
https://drive.google.com/file/d/0B3r17kL08B7QdW92UU1ZT2gwU1k/edit?usp=sharing

I'll remove them in a day or two.

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by Devon Ryan92k

Cool. 

ADD REPLYlink written 5.3 years ago by Ashutosh Pandey11k

thanks a lot !!

please let me know, which chromosomes you have included in index?

all 22+X+Y+M ?

also tell me the version, hg38 ?

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by cvu140
1

GRCh38, which for UCSC includes all of the chromosomes and unplaced contigs and I believe alternate alleles as well.

ADD REPLYlink written 5.3 years ago by Devon Ryan92k

BTW, that requires ~6 gigs of RAM to index.

ADD REPLYlink written 5.3 years ago by Devon Ryan92k

I tried it with 8GB RAM. don't know what was the problem

Thanks a lot again. i've downloaded files.

 

 

 

ADD REPLYlink written 5.3 years ago by cvu140

As mentioned below, a GRCh38 reference hasn't been made by Ensembl yet, so I can only offer the UCSC version.

ADD REPLYlink written 5.3 years ago by Devon Ryan92k

Actually, Ensembl hasn't released a version for GRCh38 yet (it'll be in the next release, number 76).

ADD REPLYlink written 5.3 years ago by Devon Ryan92k
0
gravatar for SP
4.8 years ago by
SP250
Germany
SP250 wrote:

Hi, Did you find the bug?

ADD COMMENTlink written 4.8 years ago by SP250
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