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Search: Posts Made By: GenoMax
Forum: Bioinformatics Yesterday, 07:09 AM
Replies: 2
Views: 117
Posted By GenoMax
If this is NovaSeq data then you should upgrade...

If this is NovaSeq data then you should upgrade to the latest FastQC (v. 0.11.7).
Forum: Bioinformatics Yesterday, 04:32 AM
Replies: 3
Views: 177
Posted By GenoMax
Use the links I included above. Then click on...

Use the links I included above. Then click on "nucleotide sequence" in the operations panel to the right.
Forum: Bioinformatics 01-18-2018, 01:49 PM
Replies: 3
Views: 177
Posted By GenoMax
You can find the rRNA sequences for E. coli here...

You can find the rRNA sequences for E. coli here (https://ecocyc.org/ECOLI/substring-search?type=NIL&object=ribosomal&quickSearch=Quick+Search#RNA). You can align rest of the data to the genome and...
Forum: Illumina/Solexa 01-10-2018, 10:48 AM
Replies: 2
Views: 200
Posted By GenoMax
Was the data trimmed on the sequencer? May...

Was the data trimmed on the sequencer?

May want to give sabre (https://github.com/najoshi/sabre) a try.
Forum: Illumina/Solexa 01-10-2018, 04:03 AM
Replies: 2
Views: 282
Posted By GenoMax
Hopefully you have reported this back to Illumina...

Hopefully you have reported this back to Illumina so IEM can be fixed.
Forum: Illumina/Solexa 01-09-2018, 09:38 AM
Replies: 13
Views: 1,026
Posted By GenoMax
Per sample cost is supposed to be between $25 and...

Per sample cost is supposed to be between $25 and $150 according to GenomeWeb. Not clear if that is just the cost of the sequencing reagents.
Forum: General 01-09-2018, 08:00 AM
Replies: 1
Views: 201
Posted By GenoMax
Cross-posted on Biostars:...

Cross-posted on Biostars: https://www.biostars.org/p/292580/
Forum: Illumina/Solexa 01-09-2018, 07:25 AM
Replies: 13
Views: 1,026
Posted By GenoMax
It has been in development for 2+ years so I...

It has been in development for 2+ years so I guess they have to try and recover some of the development costs. Initial cost of entry seems to be low and the whole thing appears "fool"-proof so pretty...
Forum: Illumina/Solexa 01-09-2018, 05:27 AM
Replies: 13
Views: 1,026
Posted By GenoMax
Illumina is calling "firefly" iSeq 100....

Illumina is calling "firefly" iSeq 100. Information and pre-orders are now available: https://www.illumina.com/systems/sequencing-platforms/iseq.html

Priced at $19,900 in US.
Forum: Bioinformatics 01-08-2018, 07:44 AM
Replies: 1
Views: 203
Posted By GenoMax
For reference cross-posted:...

For reference cross-posted: https://www.biostars.org/p/292377/

Copying my comment there below.

Just that part of the sequence or the whole sequence? If whole sequence is fine then you should be...
Forum: Illumina/Solexa 01-03-2018, 12:23 PM
Replies: 13
Views: 1,026
Posted By GenoMax
Dr. Keith Robinson has some thoughts in his blog...

Dr. Keith Robinson has some thoughts in his blog post (http://omicsomics.blogspot.com/2018/01/illumina-2018-preview-i-firefly.html). Perhaps consumables will be cheaper and fast turnaround would be...
Forum: Illumina/Solexa 01-03-2018, 06:38 AM
Replies: 13
Views: 1,026
Posted By GenoMax
Illumina Firefly sequencer

We can look forward to announcement of one (previously talked about) Illumina Sequencer next week at J.P. Morgan meeting.

At least one person has the sequencer in their lab:...
Forum: General 12-31-2017, 01:30 PM
Replies: 2
Views: 350
Posted By GenoMax
Elaine Mardis' annual talk at the NHGRI's Genome...

Elaine Mardis' annual talk at the NHGRI's Genome Research Series is worth watching for a capsule intro to the latest in NGS tech. I am linking talk from 2016...
Forum: Bioinformatics 12-29-2017, 01:26 PM
Replies: 4
Views: 387
Posted By GenoMax
Are you referring to building a profile HMM...

Are you referring to building a profile HMM rather than a cluster then?
Forum: Bioinformatics 12-29-2017, 12:52 PM
Replies: 4
Views: 387
Posted By GenoMax
If you just want to cluster the sequences then...

If you just want to cluster the sequences then CD-HIT (http://weizhongli-lab.org/cd-hit/) would be simpler to use.
Forum: Bioinformatics 12-26-2017, 06:22 AM
Replies: 3
Views: 660
Posted By GenoMax
Your best bet is to contact Geneious tech...

Your best bet is to contact Geneious tech support. Your question is very generic and you are using a commercial software package which is going to make it difficult to get useful help here.
Forum: Bioinformatics 12-20-2017, 11:10 AM
Replies: 1
Views: 379
Posted By GenoMax
Have you tried using "out=" to save the results...

Have you tried using "out=" to save the results to a file.
Forum: Bioinformatics 12-19-2017, 06:13 AM
Replies: 3
Views: 637
Posted By GenoMax
It would be wise to scan (and trim as needed) the...

It would be wise to scan (and trim as needed) the data for presence of extraneous sequences. Since you are going to de novo assembly, you don't want any other sequence that does not belong to your...
Forum: Bioinformatics 12-16-2017, 04:35 PM
Replies: 3
Views: 475
Posted By GenoMax
I would suggest that you get hardware that makes...

I would suggest that you get hardware that makes sense (don't forget a data backup solution, it can be as simple as multiple external drives). When in-house hardware is not sufficient for a specific...
Forum: Bioinformatics 12-16-2017, 11:58 AM
Replies: 3
Views: 475
Posted By GenoMax
Devil is always in the details of how much...

Devil is always in the details of how much sequencing you would be doing. Reagent costs for sequencing add up rapidly compared to cost of the hardware you are going to buy for computing.

I am not...
Forum: Illumina/Solexa 12-15-2017, 11:30 AM
Replies: 13
Views: 1,332
Posted By GenoMax
Very likely no. See this blog post...

Very likely no. See this blog post (https://sequencing.qcfail.com/articles/positional-sequence-bias-in-random-primed-libraries/) for more.
Forum: Bioinformatics 12-15-2017, 09:35 AM
Replies: 3
Views: 377
Posted By GenoMax
You have to use fuzznuc from EMBOSS. You can use...

You have to use fuzznuc from EMBOSS. You can use web front end if you are not able to use it on the command line (e.g. http://emboss.bioinformatics.nl/cgi-bin/emboss/fuzznuc ). You may need to do it...
Forum: Bioinformatics 12-15-2017, 09:06 AM
Replies: 3
Views: 377
Posted By GenoMax
Cross-posted and answered on BioStars:...

Cross-posted and answered on BioStars: https://www.biostars.org/p/289409/
Forum: Bioinformatics 12-15-2017, 09:04 AM
Replies: 1
Views: 344
Posted By GenoMax
For an undergraduate report that description is...

For an undergraduate report that description is fine.
Forum: Illumina/Solexa 12-14-2017, 11:02 AM
Replies: 2
Views: 341
Posted By GenoMax
Over-clustered FC's may have good data for main...

Over-clustered FC's may have good data for main reads but will fail on the index reads (do you have a large number of N's or are the sequences something you do not expect to get in the index).
...
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