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Forum: Literature Watch 11-01-2013, 12:57 PM
Replies: 0
Views: 1,485
Posted By dcfargo
Stable Pausing by RNA Polymerase II

Stable Pausing by RNA Polymerase II Provides an Opportunity to Target and Integrate Regulatory Signals

http://www.cell.com/molecular-cell/abstract/S1097-2765%2813%2900717-X
Forum: Bioinformatics 08-31-2011, 09:24 AM
Replies: 9
Views: 2,090
Posted By dcfargo
You might try building a Bowtie index that...

You might try building a Bowtie index that includes the external sequence as an additional 'chromosome' and then running TopHat Fusion.
...
Forum: Bioinformatics 08-31-2011, 08:57 AM
Replies: 10
Views: 13,614
Posted By dcfargo
With one per line and every other line: awk...

With one per line and every other line:

awk '0 == (NR + 1) % 2' infile > end1 &
awk '0 == (NR + 2) % 2' infile > end2 &
Forum: Illumina/Solexa 04-21-2011, 08:27 AM
Replies: 74
Views: 46,477
Posted By dcfargo
Anyone have an estimate for the total size per...

Anyone have an estimate for the total size per run of the outfiles. For example a per year per machine storage need? Are the outfiles the same as the HiSeq (just much smaller)?
Forum: Core Facilities 03-30-2011, 05:00 AM
Replies: 5
Views: 2,883
Posted By dcfargo
.bam fastq (Illumina 1.5+ and Sanger encoded) ...

.bam
fastq (Illumina 1.5+ and Sanger encoded)
fastqc report folder
Forum: Bioinformatics 01-04-2011, 05:02 AM
Replies: 8
Views: 3,398
Posted By dcfargo
DSAP aligns to both miRBase (16) and RFam (10) if...

DSAP aligns to both miRBase (16) and RFam (10) if you have very short read data

http://dsap.cgu.edu.tw/
Forum: Bioinformatics 08-05-2010, 04:57 AM
Replies: 513
Views: 191,733
Posted By dcfargo
Please help with genome reseq parameter...

Please help with genome reseq parameter suggestion for PE 100mer data (D. melanogaster)

What are people going with as the 'default' alignment parameters/workflow?

I'm wondering if people are...
Forum: Bioinformatics 07-29-2010, 07:01 AM
Replies: 11
Views: 17,198
Posted By dcfargo
Thanks so much. Given some information may...

Thanks so much.

Given some information may be lost and we'll just have to accept that would the best model for conversion be 2 steps such as:

1) SAMtools for BAM -> SAM

2) followed by a...
Forum: Bioinformatics 07-29-2010, 06:45 AM
Replies: 11
Views: 17,198
Posted By dcfargo
Sorry for my ignorance - why might the quality...

Sorry for my ignorance - why might the quality values change?
Forum: Bioinformatics 07-29-2010, 06:23 AM
Replies: 11
Views: 17,198
Posted By dcfargo
I do care about recovery of all of the...

I do care about recovery of all of the information.

I'd like to essentially recover all the initial text information that went into making the BAM file.
Forum: Bioinformatics 07-29-2010, 05:02 AM
Replies: 11
Views: 17,198
Posted By dcfargo
Stand Alone Bam to FASTQ

Does anyone have a suggested best practice utility for this?
Forum: Bioinformatics 05-28-2010, 05:53 AM
Replies: 4
Views: 5,004
Posted By dcfargo
The trans-ABySS 'pipeline' suggests BLAT or...

The trans-ABySS 'pipeline' suggests BLAT or Exonerate.

http://www.bioperl.org/wiki/Exonerate
Forum: Bioinformatics 02-24-2010, 05:17 AM
Replies: 2
Views: 1,724
Posted By dcfargo
I'd drop the -v go with -n (perhaps make -l a...

I'd drop the -v go with -n (perhaps make -l a little longer than default) and 'titrate' the -e value using a subset of the sequences.
Forum: Bioinformatics 06-11-2009, 07:30 AM
Replies: 10
Views: 2,359
Posted By dcfargo
Is the Genome Analyzer IIX default setup going to...

Is the Genome Analyzer IIX default setup going to write over the images as part of the processing to save space?
Forum: Illumina/Solexa 03-31-2009, 05:49 AM
Replies: 3
Views: 1,801
Posted By dcfargo
Degrade uncapped RNAs and then decap or you will...

Degrade uncapped RNAs and then decap or you will sequence tRNAs.
Forum: Illumina/Solexa 03-31-2009, 05:46 AM
Replies: 2
Views: 2,480
Posted By dcfargo
We get 40-60% of the total CHIP reads to align to...

We get 40-60% of the total CHIP reads to align to unique genomic sequence (from flys).
Forum: Events / Conferences 01-28-2009, 06:55 AM
Replies: 1
Views: 2,549
Posted By dcfargo
Recomb 2009

http://www.bio5.org/recomb2009/


Any interest in getting together for a lunch/dinner to talk nextgen offline?
Forum: General 12-10-2008, 07:37 AM
Replies: 2
Views: 1,697
Posted By dcfargo
Seems like a custom SNP-Chip would pass the...

Seems like a custom SNP-Chip would pass the FDA/CLIA more readily.
Forum: Bioinformatics 10-20-2008, 08:31 AM
Replies: 11
Views: 3,348
Posted By dcfargo
Hal9000 :) We have an 8 core 32 gig machine...

Hal9000 :)

We have an 8 core 32 gig machine for 'personal' use.
Forum: Bioinformatics 08-27-2008, 05:22 AM
Replies: 19
Views: 3,629
Posted By dcfargo
I'd bring down the entire GFF file from UCSC FTP...

I'd bring down the entire GFF file from UCSC FTP downloads and then just run a shell script by chromosome with something like

File1 = chr locations
File2 = GFF file

awk '
NR==FNR{
...
Forum: Bioinformatics 08-26-2008, 10:45 AM
Replies: 19
Views: 3,629
Posted By dcfargo
If your organism is in Ensembl you can use the...

If your organism is in Ensembl you can use the Biomart tool to extract genes (or other elements) by location.
Forum: General 08-15-2008, 04:40 AM
Replies: 5
Views: 37,893
Posted By dcfargo
CLC Bio

Is anyone using the CLC Bio genomics tools? If so would you be willing to share your experiences.
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