SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Webinar on Methyl Seq data analysis in Strand NGS- Formerly Avadis NGS Strandlife Events / Conferences 1 10-21-2014 02:28 AM
Looking for a few NGS-ers willing to share a bad experience about NGS data analysis CHoyt Bioinformatics 8 12-09-2011 11:06 PM
Publicly available test NGS exome? emucaki Bioinformatics 3 01-19-2011 05:23 AM
Hands-on ngs workshop - human exome sequencing and microbial whole genome sequencing vikram Events / Conferences 0 12-08-2010 08:36 PM
FAQs & definition of terms on Assembly/MAQ etc jess Bioinformatics 2 06-03-2009 06:01 AM

Reply
 
Thread Tools
Old 07-22-2014, 09:25 AM   #1
kamilo889
Member
 
Location: Medellin- Colombia

Join Date: Jul 2014
Posts: 15
Default NGS exome FAQs

Hi all, I'm new in exome data analysis and I have few question and an Issue installing BWA-0.7.10.

1: Is necessary create a perl script to run the program since the first alignment to HG19 using bwa? or in the terminal I can work in a easier way?

2. Im triying to install BWA last version but when i run the command make appear a big mistake

camilo@camilo-G31M-S2L:~/bwa-0.7.10$ make
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o
In file included from ksw.c:29:0:
/usr/lib/gcc/i686-linux-gnu/4.8/include/emmintrin.h:31:3: error: #error "SSE2 instruction set not enabled"
# error "SSE2 instruction set not enabled"
^
ksw.c:49:2: error: unknown type name __m128i
__m128i *qp, *H0, *H1, *E, *Hmax;
^
ksw.c: In function ksw_qinit:
ksw.c:72:11: error: __m128i undeclared (first use in this function)
q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory

ksw.c:293:5: warning: implicit declaration of function _mm_cmpgt_epi16 [-Wimplicit-function-declaration]
if(UNLIKELY(!_mm_movemask_epi8(_mm_cmpgt_epi16(f, h)))) goto end_loop8;
. ^
.
.
make: *** [ksw.o] Error 1

Any idea?.
thanks a lot
kamilo889 is offline   Reply With Quote
Old 07-22-2014, 10:34 AM   #2
Bukowski
Senior Member
 
Location: Aberdeen, Scotland

Join Date: Jan 2010
Posts: 378
Default

1) No you can run things from the command line if you desire.

2) You're on a 32bit machine (i686). SSE2 instruction sets are implemented on 64bit processors.

You can run an old version of bwa on this type of hardware, 0.5x would be fine.

You'll not really be able to work on hg19 on a 32bit machine.

Source: http://sourceforge.net/p/bio-bwa/mai...@sanger.ac.uk/

Last edited by Bukowski; 07-22-2014 at 10:37 AM.
Bukowski is offline   Reply With Quote
Old 07-22-2014, 10:39 AM   #3
kamilo889
Member
 
Location: Medellin- Colombia

Join Date: Jul 2014
Posts: 15
Default

Dear Bukowski thanks lot for your reply. about the first question ... what do you recommend? however, if I create a Perl file with my program is necessary install all the programs at first step right?.
About the second, you think that is better install 64bit version?

thanks again
kamilo889 is offline   Reply With Quote
Old 07-22-2014, 03:07 PM   #4
Bukowski
Senior Member
 
Location: Aberdeen, Scotland

Join Date: Jan 2010
Posts: 378
Default

At some point you will want to sequence your analysis workflow and how you do this is up to you - Perl, bash, Python, Makefiles - whatever you like, it's up to you. And yes you need to have all the programs installed first.

To do any kind of meaningful NGS analysis with human samples you need to be working on a 64bit *operating system* with 64bit *binaries* for your applications. Many apps, especially aligners are dropping 32bit support.
Bukowski is offline   Reply With Quote
Old 07-22-2014, 05:13 PM   #5
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,885
Default

If you don't have access to a 64-bit machine then this change should allow you to compile bwa for 32-bit. Limits mentioned by Bukowski remain though. If you are working with human data then don't do this.

https://www.biostars.org/p/80351/
GenoMax is offline   Reply With Quote
Reply

Tags
bioinformactics, ngs

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:45 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO