Forum: Bioinformatics
04-28-2016, 11:50 AM
|
|
Replies: 11
Views: 9,352
|
|
Forum: Bioinformatics
06-04-2015, 09:00 AM
|
|
Replies: 3
Views: 4,221
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, 02:04 PM
|
|
Replies: 3
Views: 3,609
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, 09:09 AM
|
|
Replies: 0
Views: 1,181
|
|
Forum: RNA Sequencing
07-03-2012, 10:48 AM
|
|
Replies: 25
Views: 7,339
|
|
Forum: Bioinformatics
06-29-2012, 09:03 AM
|
|
Replies: 9
Views: 2,795
|
|
Forum: Bioinformatics
06-29-2012, 09:01 AM
|
|
Replies: 9
Views: 2,795
|
|
Forum: Bioinformatics
06-29-2012, 08:58 AM
|
|
Replies: 9
Views: 2,795
|
|
Forum: RNA Sequencing
06-27-2012, 03:02 PM
|
|
Replies: 25
Views: 7,339
|
|
Forum: RNA Sequencing
06-26-2012, 03:26 PM
|
|
Replies: 25
Views: 7,339
|
|
Forum: Bioinformatics
05-04-2012, 03:35 PM
|
|
Replies: 10
Views: 3,330
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, 11:04 AM
|
|
Replies: 9
Views: 5,131
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, 10:40 AM
|
|
Replies: 9
Views: 5,131
|
|
Forum: Introductions
07-01-2011, 10:01 PM
|
|
Replies: 5
Views: 2,266
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, 09:58 PM
|
|
Replies: 4
Views: 6,448
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, 09:15 PM
|
|
Replies: 1
Views: 2,511
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, 09:28 AM
|
|
Replies: 252
Views: 106,947
|
|
Forum: Bioinformatics
06-15-2011, 08:14 AM
|
|
Replies: 252
Views: 106,947
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, 07:57 AM
|
|
Replies: 252
Views: 106,947
|
|
Forum: Bioinformatics
06-01-2011, 11:35 PM
|
|
Replies: 13
Views: 10,204
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, 11:02 AM
|
|
Replies: 8
Views: 3,087
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, 07:56 PM
|
|
Replies: 3
Views: 5,774
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, 07:47 PM
|
|
Replies: 5
Views: 2,069
|
|
Forum: Illumina/Solexa
04-18-2011, 06:19 PM
|
|
Replies: 6
Views: 7,714
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, 05:40 PM
|
|
Replies: 10
Views: 9,927
|
