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Search: Posts Made By: lac302
Forum: Bioinformatics 05-14-2019, 10:38 AM
Replies: 1
Views: 455
Posted By lac302
You could create a local blast database of your...

You could create a local blast database of your denovo assembly and query with known ITS sequence looking for contigs with homology.

Also, is the pool of nematodes derived from a single genetic...
Forum: Sample Prep / Library Generation 05-18-2018, 12:42 PM
Replies: 13
Views: 3,562
Posted By lac302
I'm not a big fan of the 2pt standard curve used...

I'm not a big fan of the 2pt standard curve used on the Qubit. Always gave inconsistent readings. We've actually stopped using it and rely solely on NanoDrop readings for amplified libraries and...
Forum: Bioinformatics 03-06-2018, 07:47 AM
Replies: 6
Views: 1,349
Posted By lac302
Guess what?...You can copy and paste from html to...

Guess what?...You can copy and paste from html to excel.

I was making it harder than it needed to be.
Forum: Bioinformatics 03-05-2018, 09:54 AM
Replies: 6
Views: 1,349
Posted By lac302
Thanks GenoMax. We are running our NextSeq...

Thanks GenoMax. We are running our NextSeq standalone.

The html file displays the metrics per lane per sample...I'd like to have the information for each sample combined into one row, e.g. Lane...
Forum: Bioinformatics 03-05-2018, 06:53 AM
Replies: 6
Views: 1,349
Posted By lac302
parser needed for bcl2fastq2 output

I'm looking for a parser to compile basic stats from the various html/xml/text output files from NextSeq runs. Looking for a text file to archive with fastq files that includes sample name, sample...
Forum: Sample Prep / Library Generation 02-01-2018, 10:56 AM
Replies: 7
Views: 5,018
Posted By lac302
The bead based normalization used in the XT kits...

The bead based normalization used in the XT kits have always worked well in our lab and we've always normalized inputs (1ng) using a nanodrop. Considering the Flex kit but have a few questions for...
Forum: Bioinformatics 01-24-2018, 09:20 AM
Replies: 3
Views: 1,189
Posted By lac302
deinterleave_fastq.sh < interleaved.fastq f.fastq...

deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]

The directory structure is just a folder of interleaved fastq files *0001reads.fq, *0002reads.fq, etc.
Forum: Bioinformatics 01-23-2018, 12:56 PM
Replies: 3
Views: 1,189
Posted By lac302
need to deinterleave/split all fastq files within a directory

I've been using this script in the link below for several years when I need to split PE reads into separate R1 and R2 files.

https://gist.github.com/nathanhaigh/3521724

Does anyone know of a...
Forum: Metagenomics 12-05-2016, 10:36 AM
Replies: 4
Views: 3,758
Posted By lac302
^^agreed. mothur is much easier to implement

^^agreed. mothur is much easier to implement
Forum: Illumina/Solexa 10-12-2016, 12:21 PM
Replies: 6
Views: 1,333
Posted By lac302
This is why I've kept ours offline. Good to hear...

This is why I've kept ours offline. Good to hear it was a simple solution
Forum: Bioinformatics 05-27-2016, 12:51 PM
Replies: 3
Views: 2,516
Posted By lac302
simple question for you linux users...i was...

simple question for you linux users...i was running an old version of quast that was functional but warned that i needed to update the version of matplotlib i was using.

updated quast and...
Forum: Bioinformatics 04-19-2016, 06:07 AM
Replies: 3
Views: 1,125
Posted By lac302
SOAPdenovo2 or SGA for contig assembly..SSPACE...

SOAPdenovo2 or SGA for contig assembly..SSPACE for scaffolding
Forum: Illumina/Solexa 04-11-2016, 12:33 PM
Replies: 4
Views: 1,664
Posted By lac302
I've had this error a few times in the past and...

I've had this error a few times in the past and it's always been an issue with how the flowcell was seated and cleared after going through the troubleshooting found in the guide (pg111)
Forum: Sample Prep / Library Generation 04-08-2016, 09:46 AM
Replies: 14
Views: 11,482
Posted By lac302
I think Qiagen EB buffer was used. Either way...

I think Qiagen EB buffer was used. Either way these samples are fairly concentrated. I end up diluting close to 500x in water. GC content is around 48%, so no issues there.



It's definitely...
Forum: Sample Prep / Library Generation 04-07-2016, 12:26 PM
Replies: 14
Views: 11,482
Posted By lac302
Struggling with some fungal samples using Nextera...

Struggling with some fungal samples using Nextera XT. I use this kit routinely samples ranging from arabidopsis to salmonella. gDNA is extremely clean based on Nanodrop/PicoGreen and agarose gel. ...
Forum: Illumina/Solexa 04-07-2016, 10:57 AM
Replies: 68
Views: 21,898
Posted By lac302
Is this only an issue for amplicon sequencing? I...

Is this only an issue for amplicon sequencing? I haven't run a V3 600 cycle kit in a few months but have a library to sequence next week...WGS, FastQ only.

My last run worked fine even...
Forum: Bioinformatics 02-12-2016, 10:39 AM
Replies: 674
Views: 162,478
Posted By lac302
Thanks for the quick reply Brain. I'll download...

Thanks for the quick reply Brain. I'll download the updated version.
Forum: Bioinformatics 02-12-2016, 10:09 AM
Replies: 674
Views: 162,478
Posted By lac302
Perhaps I'm using an older version of bbmap but...

Perhaps I'm using an older version of bbmap but usage shows:
Usage: dedupe.sh in=<file or stdin> out=<file or stdout>

An example of running Dedupe for clustering short reads:
dedupe.sh in=x.fq...
Forum: Bioinformatics 02-11-2016, 11:30 AM
Replies: 674
Views: 162,478
Posted By lac302
sam files are an accepted input file type for...

sam files are an accepted input file type for dedupe.sh correct? Or would you recommend removing duplicates from the fastq files?

[root@g300-149-b0 bbmap]# ./dedupe.sh Um57.sam Um57_nodups.sam ...
Forum: Bioinformatics 02-10-2016, 11:48 AM
Replies: 674
Views: 162,478
Posted By lac302
Thanks for the quick reply Brian...Does bbmap...

Thanks for the quick reply Brian...Does bbmap have any SNP calling functionality? Or should I just feed these .sam files into the samtools pipeline?
Forum: Bioinformatics 02-10-2016, 11:42 AM
Replies: 674
Views: 162,478
Posted By lac302
measured via fragment analyzer

measured via fragment analyzer
Forum: Bioinformatics 02-10-2016, 07:36 AM
Replies: 674
Views: 162,478
Posted By lac302
Ouput below. This is a nextera XT fragment...

Ouput below. This is a nextera XT fragment library that I made and sequenced. Average insert size is around 900bp. I used the defualut bbmap settings adding qtrim=r and pairlen=2000

BBMap...
Forum: Bioinformatics 02-09-2016, 12:51 PM
Replies: 674
Views: 162,478
Posted By lac302
Trying out bbmap for the first time...I'm...

Trying out bbmap for the first time...I'm aligning illumina 2x275 reads to a fungal genome. Error and sub rates for the first few samples are high, around 70%. I'm assuming the high error rate is...
Forum: Illumina/Solexa 12-01-2015, 10:46 AM
Replies: 2
Views: 1,294
Posted By lac302
backordered illumina products

anybody having issues with backordered items from illumina lately? seems like every order over the last several months is backordered. at first it was just miseq reagent cartridges but now library...
Forum: Bioinformatics 11-24-2015, 12:24 PM
Replies: 14
Views: 3,670
Posted By lac302
Thanks Brian. Forgot I had Quast installed on...

Thanks Brian. Forgot I had Quast installed on this workstation. Filtering through the output files now.
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