SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 35
Search took 0.00 seconds.
Search: Posts Made By: jstjohn
Forum: Bioinformatics 04-28-2016, 10:50 AM
Replies: 11
Views: 7,324
Posted By jstjohn
As an alternative to the symlink idea, you could...

As an alternative to the symlink idea, you could just modify your environment. I had to edit/recompress boost 1.54.0 (b/c I am running gcc-4.8) as described here:...
Forum: Bioinformatics 06-04-2015, 08:00 AM
Replies: 3
Views: 3,234
Posted By jstjohn
Lightbulb UBU likes only paired reads in the BAM files

In case this helps anyone else: when I was converting TCGA RNA-seq reads to fastq format UBU complained about the presence of unpaired reads. The following was my workaround.


Split paired and...
Forum: Bioinformatics 07-24-2013, 01:04 PM
Replies: 3
Views: 2,824
Posted By jstjohn
from the javadoc

According to the javadoc:
"The median CV of coverage of the 1000 most highly expressed transcripts. Ideal value = 0."

What is confusing me though is it looks like this involves the coefficient of...
Forum: Bioinformatics 11-27-2012, 08:09 AM
Replies: 0
Views: 944
Posted By jstjohn
Quantitate study of RIN vs degradation rate for poly-A purification libraries?

Hello,
I am interested in using RNA-seq data to identify fusion genes. To do this you need a certain number of reads supporting a given fusion, maybe 10 or so. I am trying to figure out in a...
Forum: RNA Sequencing 07-03-2012, 09:48 AM
Replies: 25
Views: 6,024
Posted By jstjohn
Alright, Cole Trapnel has been working with me on...

Alright, Cole Trapnel has been working with me on this, and he identified and fixed the problem that was causing my crash at least. I believe a new version of cufflinks (2.0.2 or something) will be...
Forum: Bioinformatics 06-29-2012, 08:03 AM
Replies: 9
Views: 2,308
Posted By jstjohn
Also you might want to see if you can find that...

Also you might want to see if you can find that read in your fastq file and double check that it has quality values there. Sometimes fastq files can become screwed up by various processing steps....
Forum: Bioinformatics 06-29-2012, 08:01 AM
Replies: 9
Views: 2,308
Posted By jstjohn
Also what tophat command did you use to do the...

Also what tophat command did you use to do the mapping? Could always be a good-ol phred+33 vs phred+64 issue.
Forum: Bioinformatics 06-29-2012, 07:58 AM
Replies: 9
Views: 2,308
Posted By jstjohn
Maybe a tophat bug? I think this is the important...

Maybe a tophat bug? I think this is the important line of that error:

12/layers/all_infected_bams/1_4I_accepted_hits_RG_reorder.bam} is malformed: BAM file has a read with mismatching number of...
Forum: RNA Sequencing 06-27-2012, 02:02 PM
Replies: 25
Views: 6,024
Posted By jstjohn
Yea, that looks like the same as mine. Seems like...

Yea, that looks like the same as mine. Seems like we all tried to use the -b bias correction option. Is there a final step with bias correction that is being missed with this, or are these runs all...
Forum: RNA Sequencing 06-26-2012, 02:26 PM
Replies: 25
Views: 6,024
Posted By jstjohn
Hey there, Not that it helps you at all, but I...

Hey there,
Not that it helps you at all, but I get the same error. You aren't alone in this!


${CUFFLINKS} \
-o out/$1/cufflinks_out \
-p 4 \
--multi-read-correct \
...
Forum: Bioinformatics 05-04-2012, 02:35 PM
Replies: 10
Views: 2,659
Posted By jstjohn
cufflinks 2.0.0 source missing a header?

Has anyone had success installing the latest cufflinks (2.0.0 beta) from source? It seems like a required local header file "rounding.h" is not included in the source distribution. I have emailed...
Forum: Bioinformatics 01-04-2012, 10:04 AM
Replies: 9
Views: 4,569
Posted By jstjohn
maybe figured this out

Hello,
I noticed that the same general question was posted on stack exchange and didn't have an answer there either. To summarize I modified the max header length variable in hits.cpp (line 731 in...
Forum: Bioinformatics 01-04-2012, 09:40 AM
Replies: 9
Views: 4,569
Posted By jstjohn
Lame... I am having the same issue and it looks...

Lame... I am having the same issue and it looks like no one has responded to you. Have you figured this out yourself yet? I am wondering, are you also using this on a highly fragmented de-novo...
Forum: Introductions 07-01-2011, 09:01 PM
Replies: 5
Views: 1,880
Posted By jstjohn
I know of an old time protein structural...

I know of an old time protein structural bioinformaticist who is just now jumping ships as well. :) I think he is a lot deeper than 8 years into the field though. You're fine.
Forum: Bioinformatics 07-01-2011, 08:58 PM
Replies: 4
Views: 5,839
Posted By jstjohn
Software list

Hey,
I am currently reviewing software for this purpose so I know of quite a few options. Most of these you can just google "[prog name] simulation genome" or something and you will find them in...
Forum: Illumina/Solexa 07-01-2011, 08:15 PM
Replies: 1
Views: 2,208
Posted By jstjohn
Citation for illumina error profile

Hello. I know that Illumina has a very low indel error rate and suffers mainly from SNP errors instead. I am having trouble finding a citation to back up that intuition though, any suggestions?
Forum: Bioinformatics 06-15-2011, 08:28 AM
Replies: 252
Views: 93,015
Posted By jstjohn
Nice tests! Good to see how that /dev/fd stuff...

Nice tests! Good to see how that /dev/fd stuff works.
Forum: Bioinformatics 06-15-2011, 07:14 AM
Replies: 252
Views: 93,015
Posted By jstjohn
Actually on most *nix systems including mac and...

Actually on most *nix systems including mac and every linux I have worked on so far you can use "/dev/fd/0" as the file name when you want to output something to standard out and the program doesn't...
Forum: Bioinformatics 06-15-2011, 06:57 AM
Replies: 252
Views: 93,015
Posted By jstjohn
Hi Boetsie, I don't know about all mappers that...

Hi Boetsie,
I don't know about all mappers that output SAM format, but BWA for example can output SAM to stdout if you don't give it the -o outfile.sam option. If you are only interested in reads...
Forum: Bioinformatics 06-01-2011, 10:35 PM
Replies: 13
Views: 9,608
Posted By jstjohn
assemblathon 2

Data is now posted for Assemblathon 2, the submission date is September 1st.

http://assemblathon.org/assemblathon-2-begins-today
Forum: De novo discovery 05-31-2011, 10:02 AM
Replies: 8
Views: 2,659
Posted By jstjohn
So I assume since it is a bacteria that there...

So I assume since it is a bacteria that there aren't a lot of issues with repeats? How about high levels of structural heterozygosity in your pool of sequences?

What kind of insert sizes do you...
Forum: Bioinformatics 04-18-2011, 06:56 PM
Replies: 3
Views: 4,881
Posted By jstjohn
1. I think GATK uses the Read Group tag to...

1. I think GATK uses the Read Group tag to partition the data into separate organisms for variant calling. If you want them treated as the same sample then you give them all the same read group tag,...
Forum: Bioinformatics 04-18-2011, 06:47 PM
Replies: 5
Views: 1,610
Posted By jstjohn
http://www.ncbi.nlm.nih.gov/projects/genome/assemb...

http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml
Forum: Illumina/Solexa 04-18-2011, 05:19 PM
Replies: 6
Views: 6,741
Posted By jstjohn
For now SeqPrep outputs gziped files regardless...

For now SeqPrep outputs gziped files regardless of the name you give the output. If its just the phred scores that look weird that could be because you have ascii Phred+64 and didn't supply -6 as a...
Forum: Bioinformatics 04-18-2011, 04:40 PM
Replies: 10
Views: 8,919
Posted By jstjohn
merging scaffolds from several SOAPdenovo assemblies into a single consensus assembly

Does anyone have experience with merging scaffolds from a few assemblies into a single consensus assembly? When I run SOAPdenovo with different k cutoffs I get different resulting scaffold...
Showing results 1 to 25 of 35

 


All times are GMT -8. The time now is 05:43 PM.


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