SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 95
Search took 0.01 seconds.
Search: Posts Made By: adamdeluca
Forum: Bioinformatics 01-02-2014, 11:54 AM
Replies: 2
Views: 2,934
Posted By adamdeluca
I would map separately for each insert size, then...

I would map separately for each insert size, then merge the resulting bams for further analysis.
Forum: Bioinformatics 01-02-2014, 11:52 AM
Replies: 10
Views: 5,813
Posted By adamdeluca
I didn't have the issue, if there is no insert,...

I didn't have the issue, if there is no insert, both reads in the pair should trim to nothing. Mine did at least.

Good luck
Forum: Bioinformatics 01-02-2014, 11:47 AM
Replies: 5
Views: 3,997
Posted By adamdeluca
use the "make" command

use the "make" command
Forum: Bioinformatics 01-02-2014, 11:42 AM
Replies: 10
Views: 5,813
Posted By adamdeluca
Yes, I saw a great number of fragments with no...

Yes, I saw a great number of fragments with no insert at all.
Forum: Bioinformatics 08-20-2013, 02:18 PM
Replies: 10
Views: 5,813
Posted By adamdeluca
My sequence differed because I was seeing reads...

My sequence differed because I was seeing reads into the barcodes.
Forum: Bioinformatics 07-23-2013, 07:20 AM
Replies: 10
Views: 5,813
Posted By adamdeluca
I used cutadapt...

I used cutadapt (https://code.google.com/p/cutadapt/) for trimming. I needed to include the barcode and primers in the trimmed sequence because of how poorly my haloplex experiment worked. Hope this...
Forum: Bioinformatics 06-11-2012, 01:01 PM
Replies: 6
Views: 8,122
Posted By adamdeluca
That's what unix pipes are for. samtools...

That's what unix pipes are for.

samtools view | myprogram

If you want to write a program to directly access bam files, there is a c library (samtools) and a java library (picard).
Forum: Bioinformatics 06-11-2012, 06:55 AM
Replies: 1
Views: 6,991
Posted By adamdeluca
A wig file is very similar to a bedgraph file so:...

A wig file is very similar to a bedgraph file so:
awk '{print $1"\t"$2-1"\t"$2"\t"$3}' file.wig > file.bedgraph

also UCSC has some useful utilities like bigWigToBedGraph ...
Forum: Bioinformatics 06-11-2012, 06:48 AM
Replies: 2
Views: 1,726
Posted By adamdeluca
look into something like snpEff or Annovar

look into something like snpEff or Annovar
Forum: Bioinformatics 04-20-2012, 05:59 AM
Replies: 3
Views: 2,024
Posted By adamdeluca
I have used a tool from expressionAnalysis called...

I have used a tool from expressionAnalysis called fastq-multx. It worked pretty well for me.

http://code.google.com/p/ea-utils/
Forum: Bioinformatics 02-13-2012, 06:48 AM
Replies: 5
Views: 3,122
Posted By adamdeluca
You can use the -G option to force cufflinks to...

You can use the -G option to force cufflinks to only estimate expression of the reference transcripts you supply. Supply 1/gene.
Forum: Bioinformatics 06-27-2011, 07:53 AM
Replies: 4
Views: 5,265
Posted By adamdeluca
bigWigToBedGraph ...

bigWigToBedGraph
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
Forum: Bioinformatics 06-01-2011, 09:11 AM
Replies: 4
Views: 2,706
Posted By adamdeluca
I would: 1. use bedtools to convert bam to a...

I would:
1. use bedtools to convert bam to a bedgraph file
2. convert the bedgraph to bigwig (ucsc utility)
3. place bigwig on a web server
4. point UCSC genome browser at bigwig file
Forum: Bioinformatics 05-19-2011, 11:51 AM
Replies: 3
Views: 10,286
Posted By adamdeluca
demo.pl #! /usr/bin/perl print STDERR...

demo.pl

#! /usr/bin/perl
print STDERR "error";
print "out";



./demo.pl 2> stderr.txt | cat > stdout.txt
Forum: Bioinformatics 05-11-2011, 06:43 AM
Replies: 2
Views: 5,636
Posted By adamdeluca
genomeCoverageBed has a "-strand" flag

genomeCoverageBed has a "-strand" flag
Forum: Bioinformatics 05-05-2011, 08:49 AM
Replies: 10
Views: 7,340
Posted By adamdeluca
Exons will be duplicated for every different...

Exons will be duplicated for every different splice form of the gene. It has to do with the way UCSC stores data.

To run the bedtools merge:
mergeBed -i in.bed -d 60 > out.bed
This will combine...
Forum: Bioinformatics 05-05-2011, 07:00 AM
Replies: 10
Views: 7,340
Posted By adamdeluca
Here is a general procedure you can follow if you...

Here is a general procedure you can follow if you want to try it yourself.

1. http://genome.ucsc.edu/cgi-bin/hgTables
2. group - "Gene and Gene Prediction Tracks", track - "UCSC genes", table -...
Forum: Bioinformatics 05-02-2011, 03:55 PM
Replies: 5
Views: 3,591
Posted By adamdeluca
would something like this work (using bedtools...

would something like this work (using bedtools (http://code.google.com/p/bedtools/))?

bamToBed -i in.bam | cut -f1,2,3,6 > out.bed
Forum: Bioinformatics 03-16-2011, 08:06 AM
Replies: 4
Views: 3,090
Posted By adamdeluca
use : ./bowtie-build the local directory...

use :
./bowtie-build

the local directory is not in your path
Forum: Introductions 03-16-2011, 08:02 AM
Replies: 4
Views: 3,488
Posted By adamdeluca
I generally say it is "genetics and computers"....

I generally say it is "genetics and computers". The followup questions are usually "What is genetics?" or "So you are in IT?". Then I talk about sports.
Forum: Bioinformatics 03-16-2011, 07:27 AM
Replies: 7
Views: 2,439
Posted By adamdeluca
great questions. Let me know if you figure them...

great questions. Let me know if you figure them out.

By manually inspecting reads in these types of regions I can observe obvious miss-mapping, and obvious off-target capture.
Forum: Bioinformatics 03-16-2011, 06:53 AM
Replies: 7
Views: 2,439
Posted By adamdeluca
Limiting your reference is a bad idea as similar...

Limiting your reference is a bad idea as similar regions differing by a single base will look like a SNP if both regions are not included in the reference.

A common approach to dealing with this...
Forum: Bioinformatics 01-21-2011, 06:15 AM
Replies: 7
Views: 7,294
Posted By adamdeluca
'n' means an ambiguous base call, an unknown. An...

'n' means an ambiguous base call, an unknown. An N in a read is a mismatch, i.e. reported in the alignment as a T>N change for example. An N in the reference will cause the alignment to break (bowtie...
Forum: Bioinformatics 01-21-2011, 06:07 AM
Replies: 1
Views: 1,218
Posted By adamdeluca
look at the complementBed program in bedtools ...

look at the complementBed program in bedtools

http://code.google.com/p/bedtools/
Forum: Bioinformatics 12-07-2010, 05:04 AM
Replies: 14
Views: 7,189
Posted By adamdeluca
a strata is a set of alignments with the same...

a strata is a set of alignments with the same score i.e. all perfect matches.
Showing results 1 to 25 of 95

 


All times are GMT -8. The time now is 05:12 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO