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Forum: Bioinformatics 07-02-2013, 10:18 PM
Replies: 1
Views: 1,827
Posted By swNGS
I would also be interested in how to do this too ...

I would also be interested in how to do this too
Could you please describe what command you use to add an additional vcf as annotation source to annovar.
Thanks
Forum: Bioinformatics 06-18-2013, 02:00 PM
Replies: 8
Views: 6,966
Posted By swNGS
Okay, that's good to know. I found this...

Okay, that's good to know.
I found this description of the TruSeq adapters here
http://genomics.med.tufts.edu/documents/protocols/TUCF_Understanding_Illumina_TruSeq_Adapters.pdf

I'm using XT...
Forum: Bioinformatics 06-07-2013, 10:04 AM
Replies: 8
Views: 6,966
Posted By swNGS
Several libraries later, I have encountered...

Several libraries later, I have encountered exactly this issue with an over-sheared SureSelect library and probable adapter read-through, which aligned very poorly (bwa_mem). Agilent won't release...
Forum: Bioinformatics 05-18-2013, 01:07 PM
Replies: 5
Views: 1,810
Posted By swNGS
That sounds promising, but I think the more long...

That sounds promising, but I think the more long term option is to database all variant results, at this stage I think this would have to be just the bare necessities in the vcf, ie chr pos ref alt...
Forum: Bioinformatics 05-18-2013, 10:20 AM
Replies: 5
Views: 1,810
Posted By swNGS
Ideas how to annotate vcf with local variant freq info?

I'm hoping for some inspiration on something that I suspect is not too tricky, but I would like some pointers.

I have a targeted sequencing panel for a particular phenotypic group of disorders in...
Forum: Bioinformatics 05-08-2013, 10:17 AM
Replies: 0
Views: 989
Posted By swNGS
? --doNotWriteOriginalQuals equivalent command in GATK 2.x ?

In GATK 1.x there was an option to discard the original quality scores for a recalibrated bam using the switch:
--doNotWriteOriginalQuals
I think during TableRecalibration

Is there an equivalent...
Forum: Bioinformatics 05-04-2013, 05:31 AM
Replies: 8
Views: 6,966
Posted By swNGS
Upon examination of insert metrics generated by...

Upon examination of insert metrics generated by Picard tools, I get a small 'notch' or 'step down' in numbers of insert sizes smaller that the 150 base boundary point (2x150 PE in use), with a rapid...
Forum: Bioinformatics 04-20-2013, 02:18 AM
Replies: 4
Views: 2,109
Posted By swNGS
and the answer is that I had assumed correctly...

and the answer is that I had assumed correctly that RealignerTargetCretor needs only running once a described here: ...
Forum: Bioinformatics 04-19-2013, 11:33 AM
Replies: 4
Views: 2,109
Posted By swNGS
My bams are derived from small targeted...

My bams are derived from small targeted resequencings experiments, but coverage can be high (several thousand)
So I make it that I can merge bams (each identified with its own read group) then run...
Forum: Bioinformatics 04-19-2013, 04:49 AM
Replies: 4
Views: 2,109
Posted By swNGS
GATK - RealignerTargetCreator ? need to run for all samples in the same experiment ?

Hi,

Lets say I have 20 bams derived form the same targetted sequencing experiment, and I want to push them through the recommended GATK pipleine.

For the RealignerTargetCreator part of...
Forum: Bioinformatics 04-17-2013, 03:30 AM
Replies: 8
Views: 6,966
Posted By swNGS
SureSelect adapter trimming

Hi,

This is a simple question, but I cant find mention of whether or not to routinely trim adapter sequences from Agilent's SureSelect PE library prep kits.

Do any of you routinely apply an...
Forum: Bioinformatics 03-09-2013, 06:58 AM
Replies: 3
Views: 1,938
Posted By swNGS
small, multiple repeats of the same experiment...

small, multiple repeats of the same experiment generating a few 100's variants per sample, approx a dozen samples at a time. I would however be interested in something that can scale up to...
Forum: Bioinformatics 03-07-2013, 10:49 AM
Replies: 6
Views: 2,409
Posted By swNGS
For Haloplex, you really need to do adapter...

For Haloplex, you really need to do adapter trimming before alignment, then clip 5 bases of the ends of each read, otherwise it suffers from biasing of the wild type allele if you get a variant at a...
Forum: Bioinformatics 03-07-2013, 10:29 AM
Replies: 3
Views: 1,938
Posted By swNGS
I'm in the process of doing something similar,...

I'm in the process of doing something similar, and rather than reinventing the wheel, am looking into adapting ensembl's variant database as a means of storing vcfs derived from many similar targeted...
Forum: Bioinformatics 03-02-2013, 09:48 AM
Replies: 5
Views: 17,170
Posted By swNGS
Another consideration with respect to MiSeq...

Another consideration with respect to MiSeq reporter is that is a lot less flexible than building your pipeline yourself (if you're that way inclined), MiSeq reporter is also windows-based so when...
Forum: Bioinformatics 03-01-2013, 10:14 AM
Replies: 5
Views: 17,170
Posted By swNGS
You need to be a bit more specific about what...

You need to be a bit more specific about what sort of sequencing you're doing (eg alignment vs assembly). For alignment of small targetted resequencing projects, the i7 will be easily okay, and...
Forum: Bioinformatics 12-18-2012, 11:05 PM
Replies: 3
Views: 3,209
Posted By swNGS
Nope, I've moved onto other topics since then,...

Nope, I've moved onto other topics since then, but I would suggest getting it directly from Agilent as an existing or potential customer
Forum: Bioinformatics 12-12-2012, 12:36 PM
Replies: 3
Views: 3,199
Posted By swNGS
The following paper suggests that bowtie2 offers...

The following paper suggests that bowtie2 offers a marginal advantage over bwasw when it comes to aligning 2x250 versus 2x150. They did use simulated data however, but worth experimenting with.
...
Forum: Bioinformatics 11-12-2012, 02:03 PM
Replies: 4
Views: 2,965
Posted By swNGS
seqtk (https://github.com/lh3/seqtk) looks...

seqtk (https://github.com/lh3/seqtk) looks promising:

The following apparently trims 5 bases from the left (5' end) and 10 bases from the right (3' end):

seqtk trimfq -b 5 -e 10 in.fa > out.fa...
Forum: Bioinformatics 11-12-2012, 01:49 PM
Replies: 4
Views: 2,965
Posted By swNGS
Hi JackieBadger Thank you for your...

Hi JackieBadger

Thank you for your suggestion, I did look into Trimmomatic. As far as can see the options are as follows:

ILLUMINACLIP: Cut adapter and other illumina-specific sequences from...
Forum: Bioinformatics 11-12-2012, 11:22 AM
Replies: 4
Views: 2,965
Posted By swNGS
Trim last 'n' reads from end of variable length PE reads

Hi,

I'm hoping that this is a simple question, but I haven't found a tool to do specifically what I'm after yet.

I have illumina 2x150 PE reads. I'm using Trim-galore, which is a wrapper for...
Forum: Bioinformatics 11-09-2012, 01:52 PM
Replies: 4
Views: 2,864
Posted By swNGS
How are you generating your sequencing libraries?

How are you generating your sequencing libraries?
Forum: Bioinformatics 10-15-2012, 10:21 PM
Replies: 6
Views: 2,115
Posted By swNGS
How would that work if I have two amplicons where...

How would that work if I have two amplicons where one lies entirely within another?
I'm not sure if the image has uploaded correctly so here is a link...
Forum: Bioinformatics 10-15-2012, 01:12 PM
Replies: 6
Views: 2,115
Posted By swNGS
I'm having another stab at this question, and...

I'm having another stab at this question, and I've tried to visually represent it in an attempt to explain better what I am trying to do:

I have a library that is comprised of thousands of...
Forum: Bioinformatics 10-13-2012, 03:44 AM
Replies: 14
Views: 3,375
Posted By swNGS
Thanks to the pointers, I have now got DNG...

Thanks to the pointers, I have now got DNG running, however I seem only to get it to output to the terminal window, with the following command:

samtools mpileup -gDf $ref_genome $bam1 $bam2 $bam3...
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