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Forum: Illumina/Solexa 01-20-2016, 05:17 AM
Replies: 31
Views: 11,558
Posted By Rocketknight
This just seems like a smaller and cheaper MiSeq...

This just seems like a smaller and cheaper MiSeq with crappier 2-dye chemistry and samey runcosts then. I guess you might consider one if you didn't have a MiSeq already, but there's nothing new for...
Forum: Illumina/Solexa 01-19-2016, 12:39 PM
Replies: 31
Views: 11,558
Posted By Rocketknight
Is that inclusive of sample prep, and/or did they...

Is that inclusive of sample prep, and/or did they say what run length that was? If that's for the 75-cycle kit this isn't really a big change from MiSeq, but if that's 300-cycle and the others are...
Forum: Illumina/Solexa 01-11-2016, 03:42 PM
Replies: 31
Views: 11,558
Posted By Rocketknight
I think the only remaining question is the price...

I think the only remaining question is the price per kit. Per luc's link, it looks like it'll be a smaller, cheaper MiSeq with almost exactly the same specs.
...
Forum: Sample Prep / Library Generation 02-25-2014, 05:43 AM
Replies: 11
Views: 6,044
Posted By Rocketknight
From experience, it's totally okay to sequence...

From experience, it's totally okay to sequence these libraries. As ECO suggested, it's almost certainly adapter sequences annealing to each other. When you see this it usually means you did too many...
Forum: Bioinformatics 07-25-2013, 06:33 AM
Replies: 6
Views: 1,980
Posted By Rocketknight
In general, your total coverage target should...

In general, your total coverage target should depend on your experimental setup. As the other posters have mentioned, if you're sequencing a 50mb genome, then all of your reads should come from that...
Forum: Bioinformatics 06-20-2013, 07:52 AM
Replies: 4
Views: 1,344
Posted By Rocketknight
GATK's DepthOfCoverage can do this. Use the -L...

GATK's DepthOfCoverage can do this. Use the -L argument to specify which positions you want coverage information for....
Forum: Bioinformatics 06-20-2013, 07:41 AM
Replies: 0
Views: 1,801
Posted By Rocketknight
Predicting Cryptic Splice Sites?

Just wondering, would anyone be able to recommend software for predicting whether mutations will introduce cryptic splice sites into genes? I've come across several software packages that look like...
Forum: Bioinformatics 06-17-2013, 08:41 AM
Replies: 0
Views: 1,130
Posted By Rocketknight
Is anyone using SNPSVM?

Hi, I just came across the paper on SNPSVM (http://bioinformatics.oxfordjournals.org/content/29/11/1361) in Bioinformatics. It was showing up as one of the most-read articles this month, and it seems...
Forum: Bioinformatics 04-01-2013, 01:02 PM
Replies: 6
Views: 2,165
Posted By Rocketknight
Oh god, I'm sorry. I kept looking through that...

Oh god, I'm sorry. I kept looking through that manual and never saw that. Sorry!
Forum: Bioinformatics 04-01-2013, 11:20 AM
Replies: 6
Views: 2,165
Posted By Rocketknight
Good point. I'm interested in 454/Ion Torrent or...

Good point. I'm interested in 454/Ion Torrent or PacBio reads, so thanks for the info! I didn't realize mrfast could handle Ion Torrent reads, they're pretty specific about calling it an Illumina...
Forum: Bioinformatics 04-01-2013, 09:43 AM
Replies: 6
Views: 2,165
Posted By Rocketknight
Aligner that reports all alignments?

Hi, I'm looking for an aligner that reports multiple/all hits rather than just a single one. I know mrfast or BWA-short can do this for Illumina data, but is there any aligner that can do this that...
Forum: Illumina/Solexa 11-19-2012, 08:02 AM
Replies: 7
Views: 6,250
Posted By Rocketknight
Capture or amplicon?

Hey all, I'm looking to sequence human exons across 189 genes totalling about 700kb. Is there anyone who's tried both target capture and amplicon sequencing who could tell me which would be better...
Forum: Sample Prep / Library Generation 10-18-2012, 05:27 AM
Replies: 7
Views: 2,743
Posted By Rocketknight
Position-specific GC bias?

Hi, I've been having an unusual problem with my reads. I've been doing exome sequencing on a HiSeq 2000, but I'm getting only about 40% GC content at the start of each read, climbing to 45-50% closer...
Forum: Bioinformatics 09-25-2012, 07:58 AM
Replies: 2
Views: 1,125
Posted By Rocketknight
Determining clinical significance of variants

Hi, I'm working with human exome samples. I'm hoping to pick out any mutations that have been previously reported as clinically significant, but I'm not sure which online databases or annotation...
Forum: Bioinformatics 08-22-2012, 07:17 AM
Replies: 15
Views: 10,711
Posted By Rocketknight
Recalibration is applied to the entire BAM...

Recalibration is applied to the entire BAM equally. Here is an example.

GATK counts all examples of the sequence 'CG' in your BAM file with quality score 20 at read position 5, and it finds 1000...
Forum: Bioinformatics 08-22-2012, 03:44 AM
Replies: 15
Views: 10,711
Posted By Rocketknight
Don't worry, you can do Base Quality Score...

Don't worry, you can do Base Quality Score Recalibration when you're searching for new mutations.

BQSR only counts mutations not in dbSNP as 'sequencing errors' for statistical purposes. It does...
Forum: Sample Prep / Library Generation 08-21-2012, 08:53 AM
Replies: 5
Views: 7,927
Posted By Rocketknight
That's quite a lot of loss for one single-sided...

That's quite a lot of loss for one single-sided Ampure cleanup. Bear in mind, though, that Ampure XP cleanup will eliminate DNA under a certain size, so is it possible that the DNA loss you're...
Forum: Bioinformatics 08-20-2012, 05:48 AM
Replies: 6
Views: 2,016
Posted By Rocketknight
http://sourceforge.net/apps/mediawiki/picard/index...

http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page#Q:_Why_am_I_getting_errors_from_Picard_like_.22MAPQ_should_be_0_for_unmapped_read.22_or_.22CIGAR_should_have_zero_elements_for_un...
Forum: Bioinformatics 08-01-2012, 05:22 AM
Replies: 10
Views: 3,129
Posted By Rocketknight
Sure thing, just sent it there.

Sure thing, just sent it there.
Forum: Bioinformatics 08-01-2012, 04:54 AM
Replies: 10
Views: 3,129
Posted By Rocketknight
I tinkered with GATK-Queue, but I had a couple of...

I tinkered with GATK-Queue, but I had a couple of problems (and I'm not too familiar with Java/Scala), so in the end I just went with a simple Python script to run everything. I used Python's...
Forum: Bioinformatics 08-01-2012, 03:57 AM
Replies: 10
Views: 3,129
Posted By Rocketknight
Yep, that will work. (Edit: Make sure you have...

Yep, that will work. (Edit: Make sure you have SORT_ORDER=coordinate set when you merge, as GATK will expect your BAMs to be sorted)
Forum: Bioinformatics 08-01-2012, 03:48 AM
Replies: 10
Views: 3,129
Posted By Rocketknight
There is indeed, if you're using GATK. Make sure...

There is indeed, if you're using GATK. Make sure every BAM file has a unique read group (you can use Picard's AddOrReplaceReadGroups function), mark duplicates with Picard, then merge all the BAM...
Forum: Bioinformatics 07-23-2012, 08:11 AM
Replies: 5
Views: 2,787
Posted By Rocketknight
If you're running Linux/OSX, you can also do the...

If you're running Linux/OSX, you can also do the whole thing at the command line like this:

$ for i in `ls *.txt`; do fastq_quality_trimmer -i $i -o $i.fastq; done

This may seem very confusing...
Forum: Illumina/Solexa 06-29-2012, 09:08 AM
Replies: 7
Views: 3,923
Posted By Rocketknight
Interestingly, doing the capture with 1-2ug as...

Interestingly, doing the capture with 1-2ug as quantified by Qubit/Picogreen doesn't seem to adversely affect the capture at all, even though that sounds like it's ten times as much DNA as you'd use...
Forum: Sample Prep / Library Generation 06-28-2012, 05:43 AM
Replies: 21
Views: 9,649
Posted By Rocketknight
Awesome, but do you lose much DNA from the...

Awesome, but do you lose much DNA from the shorter Ampure incubation time? I feel like not all of it would have precipitated after 5 minutes.
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