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Forum: Bioinformatics 08-04-2013, 09:27 AM
Replies: 10
Views: 3,025
Posted By arolfe
I'd just split the genome into chunks, build the...

I'd just split the genome into chunks, build the index on each chunk, align to each, and merge the results. You'll need to do a little post-processing if you're looking to find a single best hit for...
Forum: Bioinformatics 03-28-2013, 10:24 AM
Replies: 4
Views: 3,040
Posted By arolfe
it should just work

You add the --mm flag to the command line. If there's only one copy of bowtie2 using that index on the machine, there shouldn't be any change. If there are multiple copies of bowtie2 running at the...
Forum: Ion Torrent 10-12-2012, 08:18 AM
Replies: 5
Views: 10,220
Posted By arolfe
Mostly you can use whatever tools you'd use for...

Mostly you can use whatever tools you'd use for data from another platform. The PGM gives you a FASTQ or SFF file that you can pass to your favorite mapping/assembly/whatever program.

There are...
Forum: Bioinformatics 09-28-2012, 05:18 AM
Replies: 4
Views: 1,653
Posted By arolfe
Do you know how big the target genome was? ...

Do you know how big the target genome was? What's the total size of your contigs? Maybe your assembly didn't cover the whole genome. Or it's possible that you sequenced a lot of reads from some...
Forum: Sample Prep / Library Generation 09-11-2012, 05:45 AM
Replies: 2
Views: 1,085
Posted By arolfe
Variation in the fragment size between different...

Variation in the fragment size between different transcription factors or histone markers is normal and I don't think I've ever seen a problem as a result of the magnitude change that you observe.
...
Forum: Bioinformatics 08-27-2012, 05:48 AM
Replies: 3
Views: 1,852
Posted By arolfe
Variant calling will generally use two quality...

Variant calling will generally use two quality scores: the per-base quality scores and a mapping quality score that indicates how certain the aligner was that the read belongs at that position in the...
Forum: General 08-23-2012, 07:27 AM
Replies: 5
Views: 1,722
Posted By arolfe
doesn't look like you can

pgSnp looks like it just contains information on SNPs; it's what you might get after aligning a fasta or fastq file of sequencing reads to produce a BAM file and then analyzing the BAM file with a...
Forum: General 08-15-2012, 05:13 AM
Replies: 1
Views: 965
Posted By arolfe
I don't know of a comprehensive resource either. ...

I don't know of a comprehensive resource either.

Question 1: type of sequencing/read length: in general, ChIP-Seq works well with relatively short reads- 35 or 50bp should be fine. You might want...
Forum: Ion Torrent 08-08-2012, 12:29 PM
Replies: 4
Views: 3,126
Posted By arolfe
Not ion torrent specific

This isn't an ion torrent specific problem. As the frequency of the mutation you're looking for falls near and below the sequencing error rate, things get hard. I think you need to consider an...
Forum: Bioinformatics 08-05-2012, 05:29 PM
Replies: 2
Views: 1,244
Posted By arolfe
Bowtie2, Blat, and Blast are also a...

Bowtie2, Blat, and Blast are also a possibilities.

Whatever you choose, make sure you understand how it decides what to report. Bowtie was tuned for short reads, so it will not report matches if...
Forum: Bioinformatics 08-03-2012, 05:37 AM
Replies: 3
Views: 5,948
Posted By arolfe
Why do you think it won't work on hundreds of bam...

Why do you think it won't work on hundreds of bam files? The files are sorted, so it presumably runs through all the files at once but is only looking at a little data from each file at a given...
Forum: General 07-03-2012, 04:59 AM
Replies: 3
Views: 2,489
Posted By arolfe
I'd start with the assumption that you'll change...

I'd start with the assumption that you'll change everything in the bioinformatics pipeline between the initial and final versions and that you'll do lots and lots of testing and tweaking along the...
Forum: General 06-13-2012, 02:53 PM
Replies: 11
Views: 5,181
Posted By arolfe
Wiki pages are good, as others have mentioned. ...

Wiki pages are good, as others have mentioned.

I also try to leave projects with a README file and one or more shell scripts that run the whole analysis start to finish (data collection from...
Forum: Bioinformatics 03-25-2012, 03:00 PM
Replies: 5
Views: 2,605
Posted By arolfe
Depends on how much work you want to do

If you have the time and resources for more experiments, you might evaluate your assembly by one or several of

- paired-end sequencing and looking for indels. There are a number of techniques...
Forum: Ion Torrent 12-07-2011, 01:02 PM
Replies: 7
Views: 4,233
Posted By arolfe
We've got ours. I just analyze data, so this is...

We've got ours. I just analyze data, so this is second hand: it seems to work like it should and everyone loves it because ePCR was rather tedious. Only problem so far is no 200bp kit for OneTouch.
Forum: Ion Torrent 12-07-2011, 12:52 PM
Replies: 18
Views: 10,401
Posted By arolfe
We've used the 200bp kit. It seems to work as...

We've used the 200bp kit. It seems to work as advertised and increases the maximum construct size (adapters + insert) from about 230bp to about 330bp. I don't have any data about whether the...
Forum: Bioinformatics 11-23-2011, 06:40 AM
Replies: 7
Views: 10,952
Posted By arolfe
What are the use cases where you see BGZF as...

What are the use cases where you see BGZF as useful for fasta or fastq files? It seems to only help in the random access case, eg "database" of genome sequences, but wouldn't make much difference...
Forum: Sample Prep / Library Generation 10-25-2011, 07:56 AM
Replies: 6
Views: 4,889
Posted By arolfe
I believe that different Illumina kits used...

I believe that different Illumina kits used different adapter concentrations. For example, I think the only difference between the ChIP-Seq and genomic (?) kits was a 100X difference in adapter...
Forum: Ion Torrent 10-17-2011, 08:30 AM
Replies: 9
Views: 4,059
Posted By arolfe
We're sequencing constructs that start with a...

We're sequencing constructs that start with a 6mer barcode followed by a standard sequence and haven't seen any problems with the lack of sequence diversity in the reads.

I think the Ion Torrent...
Forum: General 10-13-2011, 09:38 AM
Replies: 4
Views: 2,975
Posted By arolfe
Genomax gave you good advice. For storage, you...

Genomax gave you good advice. For storage, you might consider Gluster, which let's you aggregate storage space from a set of servers into a single filesystem. This might simplify your storage...
Forum: Sample Prep / Library Generation 09-30-2011, 05:45 AM
Replies: 5
Views: 12,228
Posted By arolfe
Don't consider this the authoritative answer, but...

Don't consider this the authoritative answer, but I can think of two possible reasons:

1) Sequencing may work better with more uniform fragment sizes. I've heard varying claims about this on...
Forum: General 09-21-2011, 08:06 AM
Replies: 4
Views: 3,859
Posted By arolfe
I haven't tried this with IGV, but with other...

I haven't tried this with IGV, but with other genome visualizers, I've exported as SVG and then opened the file in Inkscape (an Illustrator clone; SVG is its native format). You'll need to "UnGroup"...
Forum: Genomic Resequencing 09-19-2011, 09:45 AM
Replies: 5
Views: 5,178
Posted By arolfe
The ENCODE project used HeLa cells, among others....

The ENCODE project used HeLa cells, among others. You could try doing an assembly from the chip-seq, rna-seq, and control datasets they've published. It'd probably be fragmented, but you might be...
Forum: Bioinformatics 09-07-2011, 06:16 AM
Replies: 5
Views: 3,778
Posted By arolfe
You have at least two options: 1) figure out...

You have at least two options:

1) figure out what dotfiles are being used when your job is executed and modify those. I'd save this for the next time you're bored.

2) set PATH in your job. ...
Forum: Bioinformatics 09-07-2011, 04:26 AM
Replies: 5
Views: 3,778
Posted By arolfe
If you qsub a script that does "echo $PATH", does...

If you qsub a script that does "echo $PATH", does it include the path to bowtie? It's possible that your dotfiles (eg, .bashrc) set the PATH differently for an interactive session.
Showing results 1 to 25 of 29

 


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