How to get hg19.fa?

[ninad]

I am trying to download a reference genome hg19 from UCSC site.
I tried to convert hg19.2bit to hg19.fa by twoBitToFa on UCSC tools.
It said "cannot execute binary file".
then I tried
"cat chr1.fa chr2.fa chr3.fa chr4.fa chr5.fa chr6.fa chr7.fa chr8.fa chr9.fa chr10.fa chr11.fa chr12.fa chr13.fa chr14.fa chr15.fa chr16.fa chr17.fa chr18.fa chr19.fa chr20.fa chr21.fa chr22.fa chrX.fa chrY.fa >hg19.fa"
But when I used this hg19.fa in bwa, it said
"[bwa_index] fail to open file 'hg19.fa'. Abort!
Aborted"

I am still not able to get any reference sequence build.

Note: I am using Linux and am a beginner.

[ulz_peter]

I actually did the exact same command for generating my hg19.fa file and it worked perfectly...
Are you sure you put the right path of the file as argument for bwa?

[ninad]

Yes, in fact I am in the same directory. Here is the command,
"bwa index -a bwtsw -p hg19_bwa hg19.fa "

Otherwise, have you used the twoBitToFa of UCSC?
Is there any other source for this file?

[sdvie]

Just a recommendation, I would not use the "alternative name prefix" option -p . It helps to keep it simple. Also, in the following commands you will typically have to specify the base file (hg19.fa) which then points at all the other aligner-specific indices (in the same directory).

So this should be sufficient:

bwa index -a bwtsw hg19.fa

[ninad]

Thanks sdvie for the suggestion.

Some1 please help asap. Can anyone upload a genome on rapidshare and share the link? I mean sounds ridiculous, but is there any other sophisticated way?

Or please help about twoBitToFa usage.

[sdvie]

You can get the utility program TwoBitToFa from here:

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

Once you downloaded it, you must change permissions first to allow it to be executed as a program.

Then you execute it from a terminal:

without arguments to see the options:

$ /path/to/twoBitToFa

twoBitToFa - Convert all or part of .2bit file to fasta
usage:
   twoBitToFa input.2bit output.fa
options:
   -seq=name - restrict this to just one sequence
   -start=X  - start at given position in sequence (zero-based)
   -end=X - end at given position in sequence (non-inclusive)
   -seqList=file - file containing list of the desired sequence names 
                    in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189
                    where coordinates are half-open zero-based, i.e. [start,end)
   -noMask - convert sequence to all upper case
   -bpt=index.bpt - use bpt index instead of built in one
   -bed=input.bed - grab sequences specified by input.bed. Will exclude introns

Sequence and range may also be specified as part of the input
file name using the syntax:
      /path/input.2bit:name
   or
      /path/input.2bit:name
   or
      /path/input.2bit:name:start-end

You will only need to execute the simple command:

$ /path/to/twoBitToFa /path/to/hg19.2bit /path/to/hg19.fa

Good luck.

[ninad]

Thanks sdvie. But I had already gone through these steps. unfortunately, my linux is i686 and not x86_64.
Thats why it could not execute the binary I suppose.

Now, I only have the option of "cat chr*.fa", which did not work.
I am still stuck to obtain human reference genome hg19!!!

[raonyguimaraes]

Just download it from here:

hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz

them

tar -zxvf chromFa.tar.gz

and

cat chr*.fa > hg19.fa

Done!

[ninad]

Thanks raonyguimaraes,
but I already tried that and it is still giving the same problem.

~/chromFa$ cat *.fa >hg19s.fa

command:

~/chromFa$ bwa index -a bwtsw hg19s.fa

Then this was output:

[bwa_index] fail to open file 'hg19s.fa'. Abort!
Aborted

This is not working right....

[raonyguimaraes]

Found a similar question http://seqanswers.com/forums/archive...hp/t-5236.html

I have no idea whats going on... Check the version of your bwa

[sdvie]

unprobable, but: enough memory available?

[raonyguimaraes]

Could be http://seqanswers.com/forums/archive...p/t-10766.html

Try to use a small file, index only the chr1.fa

[ulz_peter]

I tried to reproduce the error but it worked perfectly with new downloaded chr*.fa files...

Is it possible that you have no read permissions on the file?
My bwa version is 0.5.9-r16

Besides that I can't think of anything else...

[ninad]

I went through this even earlier, but I am not getting segmentatioon fault. I also have the latest version of bwa 0.5.7.

I am clueless too.

[ninad]

@peter
I will try using the mentioned specifications by you Peter. my bwa is 0.5.7 (r1310)

@raonyguimaraes-
I have tried using chr1.fa file and it works perfectly fine.
My hg19.fa file is 3 GB big. So considering the bwa indexing limit of 4 GB, it should still work.

I have checked permissions for the file, they are perfectly fine.
I believe the problem is either in concatenation or size limit. I have used cat in both above mentioned ways and its now resolved.
I dont know what can be any other problem.

@sdvie -How to check whether enough memory is available or not?