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Search: Posts Made By: kmcarr
Forum: Bioinformatics 09-14-2018, 05:11 AM
Replies: 1
Views: 384
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, 05:24 AM
Replies: 1
Views: 446
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, 05:51 AM
Replies: 2
Views: 502
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, 06:10 AM
Replies: 1
Views: 1,235
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, 04:40 AM
Replies: 4
Views: 738
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, 07:31 AM
Replies: 4
Views: 572
Posted By kmcarr
microgirl, What plate reader are you using?

microgirl,

What plate reader are you using?
Forum: Bioinformatics 05-10-2018, 04:18 AM
Replies: 1
Views: 294
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, 09:43 AM
Replies: 1
Views: 2,902
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, 06:13 AM
Replies: 7
Views: 1,403
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, 07:15 AM
Replies: 6
Views: 989
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, 06:31 AM
Replies: 1
Views: 606
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, 07:24 AM
Replies: 3
Views: 877
Posted By kmcarr
Someone who just bought a NovaSeq.

Someone who just bought a NovaSeq.
Forum: Oxford Nanopore 01-30-2018, 04:42 AM
Replies: 3
Views: 1,146
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, 01:17 PM
Replies: 5
Views: 637
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, 06:26 AM
Replies: 9
Views: 1,373
Posted By kmcarr
Make the 's' in Truseq uppercase (TruSeq)

Make the 's' in Truseq uppercase (TruSeq)
Forum: Bioinformatics 11-13-2017, 04:38 AM
Replies: 6
Views: 1,248
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, 06:35 AM
Replies: 5
Views: 961
Posted By kmcarr
Have the reads been trimmed?

Have the reads been trimmed?
Forum: Illumina/Solexa 10-03-2017, 05:12 AM
Replies: 2
Views: 702
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, 07:51 AM
Replies: 5
Views: 787
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, 05:18 AM
Replies: 1
Views: 457
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, 05:08 AM
Replies: 5
Views: 787
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, 10:06 AM
Replies: 5
Views: 1,550
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...
Forum: Bioinformatics 09-15-2017, 05:08 AM
Replies: 7
Views: 1,737
Posted By kmcarr
What about the case where there is more than one...

What about the case where there is more than one sequence which match the longest length? Save all? Only the first or last?
Forum: Illumina/Solexa 09-05-2017, 05:53 AM
Replies: 17
Views: 1,550
Posted By kmcarr
For any low quality or low quantity RNA samples...

For any low quality or low quantity RNA samples our core does not use TruSeq. We have had good results with the RNA-Seq library kits from NuGEN (http://www.nugen.com/products/rna-seq). For the sample...
Forum: Bioinformatics 08-17-2017, 05:35 AM
Replies: 1
Views: 593
Posted By kmcarr
Unless it is explicitly stated that a reported...

Unless it is explicitly stated that a reported DNA sequence is presented in a 3' to 5' orientation it is accepted convention that all DNA sequences are written 5' to 3'. All sequence data reported by...
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