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Forum: Bioinformatics 08-03-2015, 07:47 AM
Replies: 0
Views: 959
Posted By Ben Langmead
New MOOC: Algorithms for DNA Sequencing

Hi all,

This is a brief note to call your attention to an online course I teach monthly on Coursera (www.coursera.org) called Algorithms for DNA Sequencing (https://www.coursera.org/course/ads1)...
Forum: Bioinformatics 03-30-2014, 11:39 AM
Replies: 0
Views: 2,480
Posted By Ben Langmead
Flexible isoform-level differential expression analysis with Ballgown

Hi all,

On behalf of myself and co-authors (Alyssa Frazee (http://alyssafrazee.com/) and Jeff Leek (http://www.biostat.jhsph.edu/~jleek/) in particular), I wanted to call people's attention to a...
Forum: Academic/Non-Profit Jobs 09-04-2013, 10:01 PM
Replies: 0
Views: 4,946
Posted By Ben Langmead
JHU Computer Science: Postdoc in analysis of big sequencing data

Applications are invited for an open Postdoctoral Fellow position. The postdoc will work with myself (Langmead (http://www.cs.jhu.edu/~langmea/index.shtml)) and colleagues at Johns Hopkins...
Forum: Academic/Non-Profit Jobs 09-12-2012, 07:03 AM
Replies: 0
Views: 1,235
Posted By Ben Langmead
Postdoc in Langmead and Salzberg labs at Johns Hopkins Univ.

Applications are invited for an open Postdoctoral Fellow position in the laboratories of Dr. Ben Langmead and Dr. Steven L Salzberg at Johns Hopkins University. The researcher will investigate topics...
Forum: Academic/Non-Profit Jobs 06-28-2012, 01:47 PM
Replies: 0
Views: 953
Posted By Ben Langmead
Bioinformatics Engineer: Johns Hopkins University

We are seeking (http://epigenetics.jhu.edu/?section=people) a motivated bioinformatics engineer to play a key role in the pioneering research program of The Epigenetics Center of the Institute for...
Forum: Academic/Non-Profit Jobs 05-29-2012, 10:00 AM
Replies: 0
Views: 1,584
Posted By Ben Langmead
Bioinformatics Analyst: Johns Hopkins University

We are seeking a motivated bioinformatics analyst to play a key role in the pioneering research program of The Epigenetics Center of the Institute for Basic Biomedical Sciences...
Forum: RNA Sequencing 03-02-2011, 05:40 PM
Replies: 4
Views: 2,567
Posted By Ben Langmead
Hi Adam, Can you send me the log of your...

Hi Adam,

Can you send me the log of your run? (Myrna prints out a message at the end indicating what the output-dump file is named.) Also, can you send me the count_table.txt file from the run?...
Forum: Bioinformatics 11-08-2010, 05:07 AM
Replies: 11
Views: 7,227
Posted By Ben Langmead
I assume this is a question more about TopHat...

I assume this is a question more about TopHat than Bowtie, since Bowtie doesn't build WIGs. You're probably better off re-posting this question with "TopHat" in the subject, or making a feature...
Forum: General 10-19-2010, 04:49 PM
Replies: 16
Views: 4,037
Posted By Ben Langmead
Hi Michael, Yes, it's best to install...

Hi Michael,



Yes, it's best to install 'bowtie' and 'soapsnp' at the same path on all nodes, including the server. It's not strictly necessary to install those tools on the server at all, but...
Forum: Bioinformatics 10-05-2010, 08:30 AM
Replies: 3
Views: 2,137
Posted By Ben Langmead
Hi Jamal, Looks like there's a space between...

Hi Jamal,

Looks like there's a space between "-" and "X" in the "- X 400" part of your command. If you remove the space ("-X 400"), I think the command should work.

Thanks,
Ben
Forum: General 09-22-2010, 09:37 AM
Replies: 3
Views: 1,419
Posted By Ben Langmead
I found some on YouTube recently. There are some...

I found some on YouTube recently. There are some recorded lectures from NIH. This seems most relevant to your question:

http://www.youtube.com/watch?v=g0vGrNjpyA8&feature=related

But there...
Forum: RNA Sequencing 09-21-2010, 08:21 AM
Replies: 8
Views: 2,399
Posted By Ben Langmead
Hi Serena, Sorry for the delay, I will look...

Hi Serena,

Sorry for the delay, I will look into this ASAP. Could you send me the complete output from myrna_local? You can email it to me if you like (blangmea at jhsph.edu).

Thanks,
Ben
Forum: RNA Sequencing 09-17-2010, 07:57 AM
Replies: 4
Views: 2,779
Posted By Ben Langmead
Hi Serena, Is this still a problem? I saw...

Hi Serena,

Is this still a problem? I saw your other post which seemed to indicate that you had got further. If it's still a problem, I'll take a look soon.

Ben
Forum: RNA Sequencing 09-17-2010, 07:53 AM
Replies: 8
Views: 2,399
Posted By Ben Langmead
Hi Serena, Good catch! - we are using an...

Hi Serena,

Good catch! - we are using an older version of the format string in that manifest file. Our mistake won't affect how Myrna determines each URL's group unless one of the --pool*...
Forum: RNA Sequencing 09-17-2010, 07:01 AM
Replies: 8
Views: 2,399
Posted By Ben Langmead
Hi Serena, * Error in...

Hi Serena,


* Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") :
* contrasts can be applied only to factors with 2 or more levels


Looks like your input is all of the same group...
Forum: RNA Sequencing 09-16-2010, 08:11 AM
Replies: 4
Views: 2,779
Posted By Ben Langmead
* Align.pl: Running:...

* Align.pl: Running: /home/Serena/myrna-1.0.9/bin/linux64/bowtie --partition 1000000 --mm -t --hadoopout --startverbose -m 1 -n 5 -l 10 -q -I 450 -X 550 --12 .tmp.Align.pl.4432.Normal-Subject1-Lane1...
Forum: Bioinformatics 08-23-2010, 01:01 PM
Replies: 15
Views: 15,041
Posted By Ben Langmead
And when you align them as unpaired reads, the...

And when you align them as unpaired reads, the effective insert sizes you observe are in the 200-300 range?

Can you please post the full commands used to run Bowtie in unpaired and paired modes,...
Forum: Bioinformatics 08-23-2010, 12:55 PM
Replies: 15
Views: 15,041
Posted By Ben Langmead
Hi Rahul, Are you sure the -I and -X options...

Hi Rahul,

Are you sure the -I and -X options encompass (or mostly encompass) the distribution of insert sizes in your sequencing library?

Ben
Forum: Bioinformatics 08-23-2010, 06:27 AM
Replies: 4
Views: 5,301
Posted By Ben Langmead
Hi Xinwu, I'm not sure why a shared...

Hi Xinwu,

I'm not sure why a shared filesystem isn't a good solution -- it works for me, and is way more convenient than installing on each node. As for easy installation: we include a script...
Forum: Bioinformatics 08-16-2010, 07:17 PM
Replies: 28
Views: 13,147
Posted By Ben Langmead
That set of options works for me. Does your job...

That set of options works for me. Does your job fail on step 2 or step 3? Your earlier post said step 2 but your newer one said step 3.

Could you send me the "stderr" and "syslog" logs from one...
Forum: Bioinformatics 08-16-2010, 07:01 PM
Replies: 28
Views: 13,147
Posted By Ben Langmead
Hi Serena, Please send me the exact command...

Hi Serena,

Please send me the exact command used.

Thanks,
Ben
Forum: Bioinformatics 08-16-2010, 05:05 PM
Replies: 2
Views: 1,330
Posted By Ben Langmead
Hi, --best mode isn't necessarily slower...

Hi,

--best mode isn't necessarily slower than the default mode, though it is slower much of the time.

The difference observed between -n 2 and -n 3 mode is likely due to the backtracking limit,...
Forum: General 08-16-2010, 07:53 AM
Replies: 16
Views: 4,037
Posted By Ben Langmead
Hi Michael, You'll have to specify...

Hi Michael,



You'll have to specify input and output directories using --input and --output as well. Depending on your version of Hadoop and how it's set up, you may need to specify HDFS URLs...
Forum: Bioinformatics 08-11-2010, 08:36 AM
Replies: 28
Views: 13,147
Posted By Ben Langmead
Yikes, that's odd. Can you send me the manifest...

Yikes, that's odd. Can you send me the manifest file you were using? I'll try to recreate this and let you know what I find. (I did encounter some issues with memory exhaustion when I moved over...
Forum: Bioinformatics 08-10-2010, 07:05 AM
Replies: 21
Views: 12,075
Posted By Ben Langmead
Hi Iris, Paired-end alignment against the...

Hi Iris,

Paired-end alignment against the transcriptome is tricky, because the distance between the mates in genome space is affected both by fragment length, and on the "shape" of the...
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