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Forum: Sample Prep / Library Generation 11-01-2018, 05:20 AM
Replies: 4
Views: 238
Posted By kmcarr
I have only ever used the BluePippin so can't...

I have only ever used the BluePippin so can't make a comparison. I can say that I regularly isolated 200bp fragments using the BluePippin and was more than satisfied with the results.
Forum: Sample Prep / Library Generation 10-31-2018, 11:08 AM
Replies: 4
Views: 238
Posted By kmcarr
We purchased a BluePippin long ago and it has...

We purchased a BluePippin long ago and it has always had the ability to resolve both long and short fragments, dependent upon which gel cassette and program was run. What the BluePippin has that the...
Forum: Illumina/Solexa 10-31-2018, 11:01 AM
Replies: 1
Views: 211
Posted By kmcarr
Yes. An 'N'. Other than that no.

Yes. An 'N'. Other than that no.
Forum: Bioinformatics 09-14-2018, 06:11 AM
Replies: 1
Views: 434
Posted By kmcarr
Robert, No, there is no additional...

Robert,

No, there is no additional filtering. The %PF column is telling you what percentage of the original (Raw) clusters those reported PF clusters represent. You could back calculate from the...
Forum: Bioinformatics 08-27-2018, 06:24 AM
Replies: 1
Views: 498
Posted By kmcarr
Jeff, Always pre-process read data before...

Jeff,

Always pre-process read data before downstream analysis. This includes adapter trimming and quality filtering even if you don't expect to find much if any adapter.

As an aside you should...
Forum: Bioinformatics 08-06-2018, 06:51 AM
Replies: 2
Views: 533
Posted By kmcarr
This result indicates that your library included...

This result indicates that your library included a large percentage of fragments with insert size less than or equal to 200bp in length. The way Trimmomatic paired end trimming operates (by default)...
Forum: General 06-13-2018, 07:10 AM
Replies: 1
Views: 1,323
Posted By kmcarr
Based on the completely non-rigorous analysis of...

Based on the completely non-rigorous analysis of project submissions to our core I would say that 16S (and other amplicon) sequencing is nowhere near dead.
Forum: Illumina/Solexa 05-24-2018, 05:40 AM
Replies: 4
Views: 817
Posted By kmcarr
Not surprising for bacterial RNA-Seq. Bacteria...

Not surprising for bacterial RNA-Seq. Bacteria will transcribe large tracks of their genome from both strands, in polycistronic primary transcripts which may overlap. The implication is that reads...
Forum: Sample Prep / Library Generation 05-11-2018, 08:31 AM
Replies: 4
Views: 623
Posted By kmcarr
microgirl, What plate reader are you using?

microgirl,

What plate reader are you using?
Forum: Bioinformatics 05-10-2018, 05:18 AM
Replies: 1
Views: 302
Posted By kmcarr
The option "-ubam" directs intersectBed to write...

The option "-ubam" directs intersectBed to write the output as uncompressed BAM. Since your input was undoubtedly compressed it's not surprising that the uncompressed output is larger even if it...
Forum: 454 Pyrosequencing 04-23-2018, 10:43 AM
Replies: 1
Views: 3,442
Posted By kmcarr
Wow, time to fire up the WayBack Machine Mr....

Wow, time to fire up the WayBack Machine Mr. Peabody.

Yes, 454 "Paired End" technology is similar in design to Illumina Mate Pair tech. A large fragment is circularized with a linker, the circular...
Forum: Illumina/Solexa 03-12-2018, 07:13 AM
Replies: 7
Views: 1,422
Posted By kmcarr
Here's another doc from Illumina...

Here's another doc from Illumina (https://www.illumina.com/content/dam/illumina-marketing/documents/products/techspotlights/cmos-tech-note-770-2013-054.pdf) which also describes the CMOS flow cell...
Forum: Bioinformatics 03-06-2018, 08:15 AM
Replies: 6
Views: 1,029
Posted By kmcarr
Hello lac302, I have attached a perl script...

Hello lac302,

I have attached a perl script I use for this purpose, however when dealing with NextSeq run data the stats are still divided by lane. The script reads the DemultiplexingStats.xml and...
Forum: Bioinformatics 03-05-2018, 07:31 AM
Replies: 1
Views: 631
Posted By kmcarr
Hi Taylor, Could you explain a bit more what...

Hi Taylor,

Could you explain a bit more what you mean when you say 'fuzznuc did not permit variable sequence inputs using the traditional bracketed nomenclature.'? Perhaps I am misunderstanding,...
Forum: Illumina/Solexa 02-09-2018, 08:24 AM
Replies: 3
Views: 918
Posted By kmcarr
Someone who just bought a NovaSeq.

Someone who just bought a NovaSeq.
Forum: Oxford Nanopore 01-30-2018, 05:42 AM
Replies: 3
Views: 1,304
Posted By kmcarr
Fuellen, I'll address the RNA storage...

Fuellen,

I'll address the RNA storage question first since that is the easiest. Freezing is just one method for long(ish) term preservation of RNA prior to library prep. RNA Stabilization reagents...
Forum: Bioinformatics 01-20-2018, 02:17 PM
Replies: 5
Views: 649
Posted By kmcarr
In this situation you want to use...

In this situation you want to use multiple_split_libraries_fastq.py http://qiime.org/scripts/multiple_split_libraries_fastq.html

From the documentation this script may be invoked on to...
Forum: Bioinformatics 12-18-2017, 07:26 AM
Replies: 9
Views: 1,459
Posted By kmcarr
Make the 's' in Truseq uppercase (TruSeq)

Make the 's' in Truseq uppercase (TruSeq)
Forum: Bioinformatics 11-13-2017, 05:38 AM
Replies: 6
Views: 1,400
Posted By kmcarr
You have the wrong sequences in your adapter...

You have the wrong sequences in your adapter file. The TruSeq Small RNA adapter sequences differ from the standard TruSeq RNA/DNA adapters. Also, you do not need the individual index sequences, just...
Forum: Bioinformatics 10-30-2017, 07:35 AM
Replies: 5
Views: 986
Posted By kmcarr
Have the reads been trimmed?

Have the reads been trimmed?
Forum: Illumina/Solexa 10-03-2017, 06:12 AM
Replies: 2
Views: 713
Posted By kmcarr
This is not directly in answer to your question,...

This is not directly in answer to your question, but is something you need to think about if you are using custom primers and still adding PhiX to your run. If you put the custom primers in the...
Forum: Bioinformatics 09-19-2017, 08:51 AM
Replies: 5
Views: 818
Posted By kmcarr
As suspected the index sequences in the...

As suspected the index sequences in the SampleSheet are in the wrong orientation.


Index1 p7 end primer showing index read (i7) primer annealed

Index (i7)...
Forum: Bioinformatics 09-19-2017, 06:18 AM
Replies: 1
Views: 471
Posted By kmcarr
Ensembl download page...

Ensembl download page (https://www.ensembl.org/info/data/ftp/index.html)

Species table in the middle of page. Type 'Xenopus' in the Filter box (right side of table header). There are links to...
Forum: Bioinformatics 09-19-2017, 06:08 AM
Replies: 5
Views: 818
Posted By kmcarr
BD, First things first; assuming that your...

BD,

First things first; assuming that your libraries are standard Illumina design your barcodes are NOT part of R1. In the standard Illumina library design and run configuration the index read is...
Forum: RNA Sequencing 09-15-2017, 11:06 AM
Replies: 5
Views: 1,634
Posted By kmcarr
In one sense that is more accurate, but...

In one sense that is more accurate, but calculating coverage like this for RNA-Seq experiments is meaningless since it doesn't take into account the wide variation in transcript abundance. Within a...
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