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rei...@gmail.com
,
M. Stanley Fujimoto
3
5/4/18
a_to_g mode seg faults
I think I've got the bug fixed. Sorry for any inconvenience this has caused you. We've pushed
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a_to_g mode seg faults
I think I've got the bug fixed. Sorry for any inconvenience this has caused you. We've pushed
5/4/18
WYSNI
, …
Changjin Hong
5
11/13/17
Download GNUMAP-bs
Thank you so much it's work WYSNI Le mardi 7 novembre 2017 04:53:44 UTC+1, cj a écrit : Hi, WYSNI
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Download GNUMAP-bs
Thank you so much it's work WYSNI Le mardi 7 novembre 2017 04:53:44 UTC+1, cj a écrit : Hi, WYSNI
11/13/17
Perry
, …
tzfif...@gmail.com
9
3/9/17
Paired end
Hello, I'd also like to map paired end (DNA) as far a I understand I should: map R1, map R2, then
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Paired end
Hello, I'd also like to map paired end (DNA) as far a I understand I should: map R1, map R2, then
3/9/17
alistai...@gmail.com
, …
M. Stanley Fujimoto
6
1/26/17
Install on OSX error (gnumap-3.0.2.tgz)
We have moved gnumap to github. We will be updating the http://dna.cs.byu.edu/gnumap/ site to reflect
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Install on OSX error (gnumap-3.0.2.tgz)
We have moved gnumap to github. We will be updating the http://dna.cs.byu.edu/gnumap/ site to reflect
1/26/17
alistai...@gmail.com
5/26/16
gnumap compilation problems (Mac OSX) version
g++ -m64 -O3 -o obj/Driver.o -c src/Driver.cpp -Iinc/ -Ilib/gsl-1.14/ In file included from src/
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gnumap compilation problems (Mac OSX) version
g++ -m64 -O3 -o obj/Driver.o -c src/Driver.cpp -Iinc/ -Ilib/gsl-1.14/ In file included from src/
5/26/16
Jessie Li
,
cj
4
1/31/16
gnumaps bs error
The issue is resolved. The revised gnumaps package is available at jlab.bu.edu. On Tuesday, January
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gnumaps bs error
The issue is resolved. The revised gnumaps package is available at jlab.bu.edu. On Tuesday, January
1/31/16
Jessie Li
, …
Mark Clement
4
1/15/16
gnumapbs software link broken
Thank you so much! Jessie On Wednesday, January 13, 2016 at 5:44:03 PM UTC-8, Dr Clement wrote: It
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gnumapbs software link broken
Thank you so much! Jessie On Wednesday, January 13, 2016 at 5:44:03 PM UTC-8, Dr Clement wrote: It
1/15/16
Shahar Bracha
3/29/15
GNUMAP a-to-g running too slow
Hi, I've been trying to run GNUMAP on my fastq files with the -d flag for a-to-g detection, but
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GNUMAP a-to-g running too slow
Hi, I've been trying to run GNUMAP on my fastq files with the -d flag for a-to-g detection, but
3/29/15
Varun Gupta
,
Nathan Clement
4
6/17/14
.gmp file explanation when looking for A --> I editing events
Certainly. I'll try and answer your questions below. On Tue, Jun 17, 2014 at 1:46 PM, VG <
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.gmp file explanation when looking for A --> I editing events
Certainly. I'll try and answer your questions below. On Tue, Jun 17, 2014 at 1:46 PM, VG <
6/17/14
Varun Gupta
,
W. Evan Johnson
2
6/11/14
segmentation fault and mismatch option
CJ, Any intuition here? Thanks! Evan On Jun 11, 2014, at 11:11 AM, Varun Gupta <gupta567varun@
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segmentation fault and mismatch option
CJ, Any intuition here? Thanks! Evan On Jun 11, 2014, at 11:11 AM, Varun Gupta <gupta567varun@
6/11/14
Brent Pedersen
2/27/14
Re: gnumaps setup problem
The machines have 47GB of memory. I have made all of that available. The err log is attached. On Mon,
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Re: gnumaps setup problem
The machines have 47GB of memory. I have made all of that available. The err log is attached. On Mon,
2/27/14
saaura...@gmail.com
, …
bped...@gmail.com
4
2/20/14
error while running the gnumap-bs on paired end reads
So the MPI version is required to use the gnumaps.pl script? I get no error on running: ./
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error while running the gnumap-bs on paired end reads
So the MPI version is required to use the gnumaps.pl script? I get no error on running: ./
2/20/14
Nathan Clement
, …
Natacha P. Leitão
7
12/20/13
Version 2.2.0 just released
Can you check and see if your machine has the file: /usr/include/gnu/stubs-64.h Or if there is any
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Version 2.2.0 just released
Can you check and see if your machine has the file: /usr/include/gnu/stubs-64.h Or if there is any
12/20/13
dpry...@gmail.com
, …
Changjin Hong
3
12/12/13
Alignment of paired-end reads with gnumaps
The updated gnumap-bs pipeline has been fixed to resolve this issue. Now, it supports more general
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Alignment of paired-end reads with gnumaps
The updated gnumap-bs pipeline has been fixed to resolve this issue. Now, it supports more general
12/12/13
dpry...@gmail.com
, …
Mark Clement
4
12/10/13
FTP server seems to be down
Thanks Mark On Tuesday, December 10, 2013, W. Evan Johnson wrote: Yes, sorry for this hiccup. The
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FTP server seems to be down
Thanks Mark On Tuesday, December 10, 2013, W. Evan Johnson wrote: Yes, sorry for this hiccup. The
12/10/13
Casey
,
Nathan Clement
8
11/13/13
Running GNUMAP with FASTQ
I removed the --fast flags then it returned matches On Wednesday, November 13, 2013 12:14:14 AM UTC+1
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Running GNUMAP with FASTQ
I removed the --fast flags then it returned matches On Wednesday, November 13, 2013 12:14:14 AM UTC+1
11/13/13
Nathan Clement
11/11/13
Re: Hash table and memory requirement
Let me try and explain as best I can. There's a paper that goes into more technical detail if you
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Re: Hash table and memory requirement
Let me try and explain as best I can. There's a paper that goes into more technical detail if you
11/11/13
wolf...@g.ucla.edu
,
Nathan Clement
3
10/29/13
gnumap 3.0.2 compilation problem: -Bstatic error from gcc compiler
Thanks - after uncommenting line 74 it worked.
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gnumap 3.0.2 compilation problem: -Bstatic error from gcc compiler
Thanks - after uncommenting line 74 it worked.
10/29/13
nandy...@gmail.com
,
Nathan Clement
2
2/13/13
multiple hits
If a single read aligns to multiple regions, the output will print to all the best locations. ie: if
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multiple hits
If a single read aligns to multiple regions, the output will print to all the best locations. ie: if
2/13/13
Bogdan Tanasa
,
Nathan Clement
2
11/11/11
reads that align to multiple places
See below. Nathan On Nov 4, 2011, at 3:00 PM, Bogdan Tanasa wrote: > Dear all, > > please
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reads that align to multiple places
See below. Nathan On Nov 4, 2011, at 3:00 PM, Bogdan Tanasa wrote: > Dear all, > > please
11/11/11
mbendall
,
Nathan Clement
3
11/2/11
Converting FASTQ quality scores
Nathan- Just ran a few analyses, everything looks great. Thanks! Matthew On Sat, Oct 29, 2011 at 6:57
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Converting FASTQ quality scores
Nathan- Just ran a few analyses, everything looks great. Thanks! Matthew On Sat, Oct 29, 2011 at 6:57
11/2/11
alexandre...@gmail.com
,
Nathan Clement
2
10/29/11
ld: unknown option: -Bstatic
This is an issue with static and/or dynamic linking in c++. If you edit the Makefile, on about line
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ld: unknown option: -Bstatic
This is an issue with static and/or dynamic linking in c++. If you edit the Makefile, on about line
10/29/11
changjin
,
Nathan Clement
2
8/19/11
need more information or manual about sam2sgr program for bisulfite alignments
See below. Nathan On Aug 19, 2011, at 12:34 PM, changjin wrote: > Hi, Nathan > > I need more
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need more information or manual about sam2sgr program for bisulfite alignments
See below. Nathan On Aug 19, 2011, at 12:34 PM, changjin wrote: > Hi, Nathan > > I need more
8/19/11
Nathan Clement
5/23/11
GNUMAP Version 2.6.0
GNUMAP users, The latest version of GNUMAP (version 2.6.0) has just bee uploaded to the website. You
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GNUMAP Version 2.6.0
GNUMAP users, The latest version of GNUMAP (version 2.6.0) has just bee uploaded to the website. You
5/23/11
W. Evan Johnson
, …
Nathan Clement
5
4/29/11
Turn off indel calling?
Yes, but previously the pair-HMM did not allow gaps. Can I add a flag to go back to this? On Apr 29,
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Turn off indel calling?
Yes, but previously the pair-HMM did not allow gaps. Can I add a flag to go back to this? On Apr 29,
4/29/11
Fatallis
,
Nathan Clement
5
3/24/11
'std::bad_alloc'
Yes the memory limit was reached, I was using 8Gb RAM, but reducing the number of processors also
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'std::bad_alloc'
Yes the memory limit was reached, I was using 8Gb RAM, but reducing the number of processors also
3/24/11
W. Evan Johnson
, …
Nathan Clement
5
3/5/11
RNA editing with GNUMAP
Nathan, thanks for doing this promptly. We need results from both editing and bisulfite ASAP! On Mar
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RNA editing with GNUMAP
Nathan, thanks for doing this promptly. We need results from both editing and bisulfite ASAP! On Mar
3/5/11
changjin
, …
W. Evan Johnson
8
3/5/11
input sequence error
Okay, maybe it's not the same. I thought illumine qseq was the same as illumina fastq. On Mar 5,
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input sequence error
Okay, maybe it's not the same. I thought illumine qseq was the same as illumina fastq. On Mar 5,
3/5/11
W. Evan Johnson
3/5/11
GNUMAP Defaults
Nathan, Can you make -p -a .9 default parameter settings for GNUMAP? To my knowledge, everyone is
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GNUMAP Defaults
Nathan, Can you make -p -a .9 default parameter settings for GNUMAP? To my knowledge, everyone is
3/5/11
W. Evan Johnson
,
Nathan Clement
3
3/1/11
SNP calling bug
Thanks Nate. Not a problem. I just filtered them out myself, but didn't want for this to confuse
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SNP calling bug
Thanks Nate. Not a problem. I just filtered them out myself, but didn't want for this to confuse
3/1/11