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Search: Posts Made By: biznatch
Forum: Bioinformatics 03-24-2014, 10:56 AM
Replies: 0
Views: 997
Posted By biznatch
Download DNA sequences for RepeatMasker track

1. I want to download the DNA sequences for the mouse mm9 RepeatMasker track from the UCSC Genome Browser. When I tried the Table Browser it got to 167 MB after ~10 minutes then stopped, having only...
Forum: Bioinformatics 03-21-2014, 01:47 PM
Replies: 6
Views: 1,507
Posted By biznatch
That's ok, and I deleted my comment because I...

That's ok, and I deleted my comment because I realized I wasn't sure if you were talking about US dollars or something else, and I also thought maybe you're factoring in the extra cost to back up...
Forum: Bioinformatics 02-24-2014, 10:02 AM
Replies: 3
Views: 1,213
Posted By biznatch
I don't use CLC but to share genome tracks I make...

I don't use CLC but to share genome tracks I make bigwigs, upload them to Galaxy (you can use your own FTP site if you have one), make track URL's for the UCSC Genome Browser then send those URL's to...
Forum: Bioinformatics 01-27-2014, 11:37 AM
Replies: 0
Views: 1,077
Posted By biznatch
How do I analyze repeats in my ChIP-seq data?

I want to look for repeats enriched in my mouse ChIP-seq data. One way is to intersect peaks with the RepeatMasker track from the UCSC Genome Browser, and I've done that (downloaded using Table...
Forum: Bioinformatics 01-24-2014, 05:26 AM
Replies: 8
Views: 2,027
Posted By biznatch
I've aligned ~50 million mouse RNA-seq reads on...

I've aligned ~50 million mouse RNA-seq reads on my 2 year old laptop (i7, 16GB RAM). It had to run overnight but it worked. So you shouldn't need something that powerful for only 20 million...
Forum: Bioinformatics 01-19-2014, 07:33 PM
Replies: 7
Views: 4,470
Posted By biznatch
Are you aligning to the correct reference/genome?...

Are you aligning to the correct reference/genome? Take some of the sequences that Bowtie isn't aligning and BLAT them, do they align?
Forum: Bioinformatics 01-08-2014, 12:57 PM
Replies: 13
Views: 2,721
Posted By biznatch
Like BLAST?

Like BLAST?
Forum: Bioinformatics 12-21-2013, 04:08 PM
Replies: 10
Views: 3,029
Posted By biznatch
I've run about two dozen RNA- and ChIP-seq...

I've run about two dozen RNA- and ChIP-seq samples and never seen the quality dip like that in the middle, are you sure that is normal? It's still in the green, it just looks weird to me.
Forum: Bioinformatics 12-02-2013, 01:45 AM
Replies: 1
Views: 1,129
Posted By biznatch
Question about what a particular Affymetrix microarray probeset is detecting

Sorry not a sequencing question exactly, but I thought this might still be a good place to ask (is there a better place to ask microarray questions?).

Most of the time if I get the target sequence...
Forum: Sample Prep / Library Generation 11-26-2013, 07:36 PM
Replies: 1
Views: 2,313
Posted By biznatch
ChIP-Seq library prep kit, Illumina vs Kapa

We are sending ChIP samples for sequencing on a HiSeq 2500. We sent some to a facility a while ago and they used an Illumina kit (http://www.illumina.com/products/chip-seq_dna_sample_prep_kit.ilmn)...
Forum: Bioinformatics 11-14-2013, 08:35 PM
Replies: 5
Views: 1,917
Posted By biznatch
Now I figured out there is a new version macs2! ...

Now I figured out there is a new version macs2! But I got that one installed :)
Forum: Bioinformatics 11-14-2013, 12:49 PM
Replies: 5
Views: 1,917
Posted By biznatch
Thank you I think it's working now, I used...

Thank you I think it's working now, I used "python setup.pl install --user". When I type "./macs14 -h" or "./macs14 --version" it prints out the help or version number correctly.
Forum: Bioinformatics 11-14-2013, 10:48 AM
Replies: 5
Views: 1,917
Posted By biznatch
I'm trying to install MACS version 1.4.2 and I...

I'm trying to install MACS version 1.4.2 and I have python version 2.7.4 installed in Ubuntu. The MACS website says Python version must be 2.6 or 2.7 and it fails to install for me saying "macs...
Forum: Bioinformatics 10-07-2013, 02:33 PM
Replies: 5
Views: 1,463
Posted By biznatch
I think I figured it out. I'm using bedtools in...

I think I figured it out. I'm using bedtools in an Ubuntu virtual machine but saved the files in Notepad++ in Windows. I think it's a newline character problem so the "+" at the end of the line...
Forum: Bioinformatics 10-07-2013, 02:26 PM
Replies: 5
Views: 1,463
Posted By biznatch
Tried that already, it also doesn't work.

Tried that already, it also doesn't work.
Forum: Bioinformatics 10-07-2013, 02:09 PM
Replies: 5
Views: 1,463
Posted By biznatch
Bedtools -s (strandedness) not working

The -s option isn't working for me with bedtools (v2.17.0). As a test I made two files each with only one line:

file1.bed
chr1 100 200 name1 0 +

file2.bed
chr1 100 200 name2 0 +

Then used...
Forum: Bioinformatics 09-05-2013, 06:57 AM
Replies: 0
Views: 1,382
Posted By biznatch
Bowtie2 error "Error reading _offs[] array"

I've used Bowtie2-build to make 2 indexes of the same genome (mm9). The first index uses all default settings for Bowtie2-build. The second index uses custom settings that should hopefully make the...
Forum: Bioinformatics 08-29-2013, 12:28 PM
Replies: 0
Views: 1,984
Posted By biznatch
Bowtie2-build settings to speed up alignment

The bowtie2-build indexer lists several performance options. I am unsure about what some of these do, and about whether they can be used to increase the performance (speed up) just the index...
Forum: Genomic Resequencing 08-29-2013, 05:50 AM
Replies: 2
Views: 1,989
Posted By biznatch
If you go to the UCSC Genome Browser and turn on...

If you go to the UCSC Genome Browser and turn on the Gap track you will see that telomeres are annotated at the ends of the chromosomes but if you zoom in the sequences are just N's.
Forum: Bioinformatics 08-08-2013, 11:15 AM
Replies: 17
Views: 7,191
Posted By biznatch
I did a little work on one set of RNA-seq data...

I did a little work on one set of RNA-seq data here's what I found, and there's some related comments.

http://seqanswers.com/forums/showthread.php?t=15870
Forum: Bioinformatics 08-06-2013, 01:02 PM
Replies: 2
Views: 5,003
Posted By biznatch
Your PLOS ONE paper only looks at histone...

Your PLOS ONE paper only looks at histone modifications. Would diffReps be appropriate to use with transcription factors that don't generate wide peaks like histone modifications? Perhaps using a...
Forum: Bioinformatics 03-12-2013, 03:59 AM
Replies: 2
Views: 810
Posted By biznatch
I don't know about visualization, but the UCSC...

I don't know about visualization, but the UCSC Table Browser can output overlaps between tracks, so if you load the bed files it can output a list of where they overlap. Bedtools can also quickly...
Forum: RNA Sequencing 03-11-2013, 06:19 AM
Replies: 8
Views: 2,042
Posted By biznatch
I don't think tophat necessarily works better...

I don't think tophat necessarily works better with 3 segments for each read, do you see that somewhere? But I know that if your sequences get too short it gets harder to get specific alignments. I...
Forum: RNA Sequencing 03-11-2013, 05:42 AM
Replies: 8
Views: 2,042
Posted By biznatch
My understanding of how Tophat works is that if...

My understanding of how Tophat works is that if it can't align the entire read it divides it into (by default) 25bp chunks and tries to align those separately. You can change the size they get split...
Forum: Epigenetics 02-25-2013, 08:34 AM
Replies: 0
Views: 1,141
Posted By biznatch
Is it ok to ChIP-Seq two samples when the ChIP worked better in one?

We want to do ChIP-Seq for RNA PolII between Control and Treatment (plus input). In the past we've done ChIP-qPCR and it's worked well. To make sure the ChIP worked equally well between Control and...
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