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Forum: Bioinformatics 09-19-2014, 07:30 AM
Replies: 18
Views: 95,498
Posted By earonesty
Global dump" is kindof ambiguous. What format...

Global dump" is kindof ambiguous. What format do you want?

Bio::IlluminaSAV can be used to make a "dump" by using JSON or YAML or whatever, and then dumping each metric to a file.
Forum: RNA Sequencing 07-15-2014, 10:18 AM
Replies: 14
Views: 31,947
Posted By earonesty
sam-stats with the -R option outputs a "skewness"...

sam-stats with the -R option outputs a "skewness" value for each transcript. Because of huge variation in reference, there's no absolute good number for this value, but you can compare the median...
Forum: Bioinformatics 06-30-2014, 01:33 PM
Replies: 0
Views: 962
Posted By earonesty
Determine ERCC presence

My one-liner of the day:

Is there ERCC spiked into my sample?

fastq-mcf n/a -l 30 $fq1 | zhead -n 100000 | bowtie -p 4 -S -m 1 --best --strata ercc92.fa - 2>&1 > /dev/null | perl -ne...
Forum: RNA Sequencing 06-24-2014, 02:05 PM
Replies: 14
Views: 31,947
Posted By earonesty
I've found that outliers in median coverage...

I've found that outliers in median coverage skewness tend to have higher variability, thus reducing the power if these samples are included in group comparisons.
Forum: RNA Sequencing 06-23-2014, 08:10 AM
Replies: 14
Views: 31,947
Posted By earonesty
also sam-stats -R cacluates coverage, bias and a...

also sam-stats -R cacluates coverage, bias and a skewness metric for rna seq. median skewness can be a single-metric summary of coverage bias per sample.

More about coverage skewness:...
Forum: Bioinformatics 05-21-2014, 08:08 AM
Replies: 44
Views: 30,386
Posted By earonesty
Or you may need to remove adaptors at the tails...

Or you may need to remove adaptors at the tails of your reads, esp if you sequenced a long read length, while keeping the Illumina fragmentation default of only 165bp. Fragment to 165, sequence at...
Forum: Bioinformatics 04-21-2014, 12:36 PM
Replies: 13
Views: 6,725
Posted By earonesty
Note: I get the same error on a pair of reads...

Note: I get the same error on a pair of reads that don't even have alignments at all (unaligned bits are set). But setting the VALIDATION_STRINGENCY=SILENT worked for me.
Forum: Bioinformatics 04-17-2014, 12:35 PM
Replies: 13
Views: 10,327
Posted By earonesty
I also see this issue. I only use 0.7.5 for...

I also see this issue. I only use 0.7.5 for "mem", not for anything else.
Forum: Bioinformatics 02-27-2014, 10:10 AM
Replies: 7
Views: 15,726
Posted By earonesty
actually there's a bug in bowtie ... a race...

actually there's a bug in bowtie ... a race condition that can make it unreliable. you should not use fifo's unless you used the patched version that supports them
...
Forum: Bioinformatics 02-18-2014, 07:40 AM
Replies: 7
Views: 15,726
Posted By earonesty
this patch fixes fifo support, and also adds...

this patch fixes fifo support, and also adds built-in gzip support to bowtie 1.0 (which remains the fastest, fastq->sam program out there)

https://github.com/earonesty/bowtie
Forum: Illumina/Solexa 10-03-2013, 06:40 AM
Replies: 1
Views: 1,844
Posted By earonesty
I use this: ...

I use this:

https://code.google.com/p/ea-utils/source/browse/trunk/clipper/contig-stats

which is more thorough.

What info do you want per contig, I can add it:

id,length, gc percent, .......
Forum: Bioinformatics 09-16-2013, 12:06 PM
Replies: 18
Views: 95,498
Posted By earonesty
1. I would be interested in the IndexMetrics file...

1. I would be interested in the IndexMetrics file (erik at q32.com) is fine

2. I would also like to try out your code (same email)

3. The LibXML reader is for parsing the RunInfo.xml into a...
Forum: Bioinformatics 06-13-2013, 06:19 AM
Replies: 10
Views: 9,487
Posted By earonesty
Parameter-sweep - comparison of clipping...

Parameter-sweep - comparison of clipping programs:

http://benthamscience.com/open/openaccess.php?tobioij/articles/V007/1TOBIOIJ.htm
Forum: Bioinformatics 06-07-2013, 09:25 PM
Replies: 29
Views: 20,457
Posted By earonesty
The CPAN module Bio::IlluminaSAV is a parser for...

The CPAN module Bio::IlluminaSAV is a parser for Perl.
Forum: Bioinformatics 06-07-2013, 09:25 PM
Replies: 18
Views: 95,498
Posted By earonesty
The CPAN module Bio::IlluminaSAV is a parser for...

The CPAN module Bio::IlluminaSAV is a parser for Perl.
Forum: Bioinformatics 06-04-2013, 10:54 AM
Replies: 17
Views: 15,817
Posted By earonesty
Lastest version passes all the relevant CPAN test...

Lastest version passes all the relevant CPAN test reports for MiSEQ and GAII data. the failed reports are on test systems that can't handle the volume of data. HiSeq passes as well, but is too...
Forum: Bioinformatics 05-20-2013, 10:17 AM
Replies: 7
Views: 8,887
Posted By earonesty
I meant as extra columns for edgeR, not as a...

I meant as extra columns for edgeR, not as a "leading gene thing". Stuff like a normalized mean and variability for each group. I've taken to moderating edgeR's results by removing results where...
Forum: RNA Sequencing 05-17-2013, 02:26 PM
Replies: 5
Views: 2,411
Posted By earonesty
reindexing didn't help. foobar$ wasn't part of...

reindexing didn't help. foobar$ wasn't part of the error... just the prompt. testing "manually" running it, instead of through our grid engine, thinking it might be some ulimit thing
Forum: RNA Sequencing 05-17-2013, 06:05 AM
Replies: 5
Views: 2,411
Posted By earonesty
Mysteriously as well, I am also having this issue...

Mysteriously as well, I am also having this issue where smaller samples complete, and some fail. Our tophat2 boxes have 60GB ram, and we're doing the run with --no-coverage-search. It I figure it...
Forum: Bioinformatics 05-01-2013, 08:24 AM
Replies: 36
Views: 19,209
Posted By earonesty
Yep. They are synonyms, and are used...

Yep. They are synonyms, and are used inconsistently.

Personally, I say "clip", when I mean "looking for adapters or other sequences and removing them off the ends of reads", and "trim" when I...
Forum: Bioinformatics 04-29-2013, 07:24 AM
Replies: 17
Views: 15,817
Posted By earonesty
Module Bio::IlluminaSAV at CPAN is available for...

Module Bio::IlluminaSAV at CPAN is available for these files. Version 1.0, release 7013 works well (prev release was missing files). You can install using:

sudo cpanm -i Bio::IlluminaSAV
Forum: Bioinformatics 04-18-2013, 07:09 AM
Replies: 13
Views: 5,431
Posted By earonesty
integers

edgeR expects integers, but many programs use estimation functions to improve transcript counts... ie: non integers. So you need to round.
Forum: Bioinformatics 11-26-2012, 08:51 AM
Replies: 7
Views: 8,887
Posted By earonesty
It *might* be informative to show a summary of...

It *might* be informative to show a summary of original expression values and variability per group - just so you can see if edgeR's being silly and might need some tweaking ... (like when expression...
Forum: The Pipeline 11-09-2012, 09:56 AM
Replies: 80
Views: 222,716
Posted By earonesty
PacBio reads, at Q8, are still quite useful for...

PacBio reads, at Q8, are still quite useful for scaffolding assemblies. Crazy to hold back data when there are lots of people who could make use of long Q14 reads right now.
Forum: Bioinformatics 09-13-2012, 01:11 PM
Replies: 1
Views: 2,942
Posted By earonesty
Tabix allows you to access a file by quering for...

Tabix allows you to access a file by quering for (for example) a chromosome and position and retrieve all the lines of that file that match your query.

Problems arise when you need to do thousands...
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