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Search: Posts Made By: DNA Sorcerer
Forum: Bioinformatics 02-23-2016, 04:51 AM
Replies: 240
Views: 83,345
Posted By DNA Sorcerer
See below. I run it for only one fo the files...

See below. I run it for only one fo the files because doing both would go over my storage quota.
Forum: Bioinformatics 02-22-2016, 12:22 PM
Replies: 240
Views: 83,345
Posted By DNA Sorcerer
testformat says:...

testformat says: illumina fastq raw single-ended 108bp

As far as I remember this was a HiSeq run.

I tried the reformat line suggested by Brian but the process stops after a while with errors....
Forum: Bioinformatics 02-22-2016, 08:49 AM
Replies: 240
Views: 83,345
Posted By DNA Sorcerer
Thank Brian, You are probably right in your...

Thank Brian,

You are probably right in your suspicion. The read files are old, probably 2011 or so, and were originally .txt and I changed to .fastq. Would this have confused BBmap?
Forum: Bioinformatics 02-19-2016, 07:06 AM
Replies: 240
Views: 83,345
Posted By DNA Sorcerer
Thanks, I'll take a closer look at the cluster's...

Thanks, I'll take a closer look at the cluster's manual and try again.
Forum: Bioinformatics 02-19-2016, 06:42 AM
Replies: 240
Views: 83,345
Posted By DNA Sorcerer
Thanks Brian, I got it run on 16 threads, but...

Thanks Brian,
I got it run on 16 threads, but after a little while I get these sort of errors:



Before this run the program suggested using ignorebadquality, which I did for this run.
Forum: Bioinformatics 02-18-2016, 11:40 AM
Replies: 240
Views: 83,345
Posted By DNA Sorcerer
Ops, I had forgotten to load java module before....

Ops, I had forgotten to load java module before. I did now, bbmap run for a couple of minutes and stopped. This is the output:
Forum: Bioinformatics 02-18-2016, 11:10 AM
Replies: 240
Views: 83,345
Posted By DNA Sorcerer
Hi Brian, I tried to run bbmap but got an...

Hi Brian,

I tried to run bbmap but got an error, and before going into debugging wanted to see if you can tell me if I have a general configuration issue in the custer (e.g. java), so I know what...
Forum: Sample Prep / Library Generation 07-23-2015, 10:54 AM
Replies: 2
Views: 2,121
Posted By DNA Sorcerer
Nextera XT for prepping Chip-Seq sample?

Hello,
Illumina suggests using their TruSeq ChipSeq kit, but I wonder if the Nextera XT should work as well for chipseq sample (mainly because we already have an XT kit). This is for yeast and we...
Forum: Bioinformatics 04-22-2013, 09:23 AM
Replies: 2
Views: 924
Posted By DNA Sorcerer
Optimal resource allocation for a heavy BLASTN run?

Hello,

I need to run BLASTN (locally) on my institution's cluster. My query contains a million short reads and DB contains an equivalent number of sequences.

What would make the run go faster?...
Forum: Ion Torrent 04-16-2013, 09:15 AM
Replies: 121
Views: 104,769
Posted By DNA Sorcerer
Just the skin, and hid the hoses and secured the...

Just the skin, and hid the hoses and secured the reagent bottles.
Forum: Sample Prep / Library Generation 01-11-2013, 09:59 AM
Replies: 1
Views: 1,180
Posted By DNA Sorcerer
I've decided to use Cells-to-cDNA by Ambion. If...

I've decided to use Cells-to-cDNA by Ambion. If someone objects to that please let me know asap!
Forum: Sample Prep / Library Generation 01-11-2013, 07:32 AM
Replies: 1
Views: 1,180
Posted By DNA Sorcerer
Experience with RNAlater samples?

I have two tubes of a precious, irreplaceable sample with approximately 20 cells of an unknown eukaryotic microbe and would like to get a transcriptome out of it. As far as I could find out, the way...
Forum: RNA Sequencing 01-09-2013, 02:57 PM
Replies: 4
Views: 1,062
Posted By DNA Sorcerer
Thanks Richard, looks like a great resource,...

Thanks Richard, looks like a great resource, bookmarked.

In this case I meant the actual sequencing service.
Forum: RNA Sequencing 01-09-2013, 01:59 PM
Replies: 4
Views: 1,062
Posted By DNA Sorcerer
RNA-seq, fast turnaround needed

I need to do a couple of transcriptomes but can't wait two months. Who is doing the job within a 4-week frame? -while keeping prices below outrageous of course-

Thanks!
Forum: General 08-26-2011, 02:00 PM
Replies: 1
Views: 1,759
Posted By DNA Sorcerer
"Lab scale" NSG sequencers

Illumina and Roche have just launched their "Junior", small-scale versions of their sequencers, both at about $150K. How long till other players do the same? (e.g. PacBio, IonT, Solid). How likely...
Forum: Illumina/Solexa 07-25-2011, 12:26 PM
Replies: 6
Views: 4,734
Posted By DNA Sorcerer
I though that library prep is done the same way...

I though that library prep is done the same way as for GAIIx.
The main differences are in throughput. Myseq has only one "lane" and gives about 1GB when doing 150bp PE in abut 27Hs. Of course myseq...
Forum: RNA Sequencing 05-12-2011, 04:04 AM
Replies: 2
Views: 2,891
Posted By DNA Sorcerer
Thank you captain. Very useful tips indeed, will...

Thank you captain. Very useful tips indeed, will read those papers.


Regards,
Forum: RNA Sequencing 05-11-2011, 09:50 AM
Replies: 2
Views: 2,891
Posted By DNA Sorcerer
How much sequencing output for chip-seq?

How much reads/bp are typically aimed for in a chip-seq experiment? Do people run one lane of GAII for one experiment? Is that more than enough?

thanks
Forum: Sample Prep / Library Generation 05-06-2011, 04:55 AM
Replies: 0
Views: 1,656
Posted By DNA Sorcerer
Enrichment/targeted sequencing using very short tags

Hello,
Would it be feasible to enrich a gDNA sample (for any NGS method) with regions that surround a specific sequence that is very short (~20bp)?

Regards,
Forum: Events / Conferences 04-15-2011, 03:23 PM
Replies: 14
Views: 5,009
Posted By DNA Sorcerer
I also got "invitations" to talk at a couple of...

I also got "invitations" to talk at a couple of conferences by "bitconferences". They use pompous names such as "1st Annual Symposium of Antiparasites" and "1st Annual World Congress of Marine...
Forum: Events / Conferences 04-10-2011, 06:56 PM
Replies: 14
Views: 5,009
Posted By DNA Sorcerer
Thanks for the insights. Is it me or we are...

Thanks for the insights.
Is it me or we are getting into a surge of these kind of "for-profit" conferences organized by obscure commercial organisations where scientific interest is just an excuse...
Forum: General 03-09-2011, 05:17 AM
Replies: 4
Views: 1,829
Posted By DNA Sorcerer
ideally (given enough depth - i.e. sufficient...

ideally (given enough depth - i.e. sufficient reads) you'll get one contig per each type of RNA molecule present in the sample (only mRNAs if you did a polyA-purification step).
Forum: General 09-23-2010, 06:47 AM
Replies: 54
Sticky: NGS Blogs
Views: 71,735
Posted By DNA Sorcerer
just came across http://snpgenotyping.info

just came across http://snpgenotyping.info
Forum: General 09-23-2010, 06:44 AM
Replies: 1
Views: 2,517
Posted By DNA Sorcerer
Sequencing BAC clones with NextGen

Is there any drawbacks of using Illumina or Solid to sequence BAC clones?

A company quoted about 10K to sequence one BAC clone (about 140Kb) using the conventional way (shotgun-sanger-assembly),...
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