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Forum: Illumina/Solexa 08-07-2020, 04:44 AM
Replies: 3
Views: 416
Posted By GenoMax
You should be able to do asymmetric runs like...

You should be able to do asymmetric runs like that. But wait for @luc or one of the experimental people to confirm for certain.

As long as there is sequenceable material left there should be no...
Forum: Sample Prep / Library Generation 08-03-2020, 12:37 PM
Replies: 4
Views: 251
Posted By GenoMax
Unique dual indexes are used in library prep. See...

Unique dual indexes are used in library prep. See this. (https://support.illumina.com/bulletins/2018/08/understanding-unique-dual-indexes--udi--and-associated-library-p.html)
Forum: Sample Prep / Library Generation 08-03-2020, 08:57 AM
Replies: 4
Views: 251
Posted By GenoMax
As long as you use unique indexes for all samples...

As long as you use unique indexes for all samples (dual indexes would be best), QC and then balance the libraries in the pool so the contents are more or less uniform, you can mix and sequence these...
Forum: Illumina/Solexa 08-03-2020, 05:39 AM
Replies: 1
Views: 219
Posted By GenoMax
You need to contact Illumina tech support. They...

You need to contact Illumina tech support. They can take a remote look at your machine otherwise ask for some files. Sounds like an hardware issue.
Forum: Bioinformatics 07-27-2020, 05:15 AM
Replies: 2
Views: 281
Posted By GenoMax
Cross-posted and answered at:...

Cross-posted and answered at: https://www.biostars.org/p/451453/
Forum: Sample Prep / Library Generation 07-16-2020, 07:31 AM
Replies: 1
Views: 514
Posted By GenoMax
I don't fully understand what you are asking but...

I don't fully understand what you are asking but is this with reference to downstream data analysis (factors to be added in model). Is that correct?
Forum: Illumina/Solexa 07-09-2020, 02:38 AM
Replies: 1
Views: 656
Posted By GenoMax
You have a set of indexes there that have a good...

You have a set of indexes there that have a good number of reads. If they don't match indexes you expect then it is a different matter. There is not much you can do about the 20% reads you are losing.
Forum: Bioinformatics 06-20-2020, 07:41 AM
Replies: 14
Views: 9,375
Posted By GenoMax
A long shot. Blast indexes changed to a new...

A long shot. Blast indexes changed to a new version as of Feb 2020. I am not sure where you are running this but if BRIG has not been updated to account for that, it may be causing this problem.
Forum: Bioinformatics 06-10-2020, 09:07 AM
Replies: 4
Views: 493
Posted By GenoMax
Looks like you are trying to do this on Windows....

Looks like you are trying to do this on Windows. That is a different can of worms. Programs like Kai Blin's are written to work on linux/macOS. While some may work on Windows there is no guarantee...
Forum: Bioinformatics 06-10-2020, 08:28 AM
Replies: 4
Views: 493
Posted By GenoMax
There is no GUI for Kai Blin's NCBI Genome...

There is no GUI for Kai Blin's NCBI Genome downloader tool so I am not sure what is crashing for you. That is a command line tool. Install and use on command line. There are thousands of bacterial...
Forum: Bioinformatics 06-08-2020, 03:09 PM
Replies: 1
Views: 640
Posted By GenoMax
Have you marked duplicate reads?

Have you marked duplicate reads?
Forum: General 05-28-2020, 06:53 AM
Replies: 1
Views: 855
Posted By GenoMax
Have you tried to use an assembly reconciliation...

Have you tried to use an assembly reconciliation tool? There may be a newer reference than this one (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1213-3) of such tools.
Forum: Bioinformatics 05-26-2020, 12:07 PM
Replies: 4
Views: 738
Posted By GenoMax
Yes it should be possible. Take a look at this...

Yes it should be possible. Take a look at this page (https://www.ncbi.nlm.nih.gov/books/NBK25498/).
Forum: Bioinformatics 05-26-2020, 09:46 AM
Replies: 4
Views: 738
Posted By GenoMax
You can check Entrezdirect ...

You can check Entrezdirect (http://bit.ly/entrez-direct)from NCBI. Use it to do pubmed database searches like this.

esearch -db pubmed -query "CDC45 [GENE]" | efetch -format abstract
Forum: Bioinformatics 05-17-2020, 09:39 AM
Replies: 3
Views: 649
Posted By GenoMax
I suggest you try "bbduk.sh" from BBMap suite...

I suggest you try "bbduk.sh" from BBMap suite instead. A guide (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) is available. You can trim out all these things in one...
Forum: Bioinformatics 05-16-2020, 01:50 PM
Replies: 3
Views: 649
Posted By GenoMax
Index sequences are never part of an actual read...

Index sequences are never part of an actual read in Illumina sequencing so you are never going to find index sequences you noted above in R1/R2 reads.

As for the poly-A and ploy-G (no signal, two...
Forum: Bioinformatics 04-30-2020, 06:31 AM
Replies: 6
Views: 520
Posted By GenoMax
You could try it out and see if it works (I have...

You could try it out and see if it works (I have a hunch it won't be perfect).

If that does not work acceptably then I suggest you run mutate.sh multiple times with new values and create new...
Forum: Bioinformatics 04-30-2020, 05:54 AM
Replies: 6
Views: 520
Posted By GenoMax
Perhaps I am missing a subtle point but since you...

Perhaps I am missing a subtle point but since you can control mutation type/rates with mutate.sh would it not be better to go with just that data (#2 in list above)? If you mix reads from mutated and...
Forum: Bioinformatics 04-30-2020, 03:02 AM
Replies: 6
Views: 520
Posted By GenoMax
It may be best to use "mutate.sh" (to look at...

It may be best to use "mutate.sh" (to look at in-line help) to introduce the mutations after you generate the reads with randomreads.sh. You will get a VCF files of changes.

I think using...
Forum: Illumina/Solexa 04-22-2020, 06:09 PM
Replies: 9
Views: 1,224
Posted By GenoMax
You really should have asked for phiX to be...

You really should have asked for phiX to be added. You should consider the fact that this run could have completely failed, if it was a bit overloaded, leaving you with no data. Raw image data is...
Forum: Illumina/Solexa 04-22-2020, 12:38 PM
Replies: 9
Views: 1,224
Posted By GenoMax
Yikes this is a really low diversity sample. Do...

Yikes this is a really low diversity sample. Do you know how much phiX (if any) was added to this sample. Did you not tell the sequence provider that these were low diversity? If you did not then it...
Forum: Illumina/Solexa 04-20-2020, 08:51 AM
Replies: 6
Views: 795
Posted By GenoMax
If we assume all 10000 cells survived. You want a...

If we assume all 10000 cells survived. You want a minimum 50000 reads per cell so that is 500M reads * 2 conditions = 1 Billion clusters/single-end reads total. Sequencing length if fixed based on...
Forum: Illumina/Solexa 04-20-2020, 08:10 AM
Replies: 6
Views: 795
Posted By GenoMax
How many cells did you submit?

How many cells did you submit?
Forum: Illumina/Solexa 04-20-2020, 07:20 AM
Replies: 6
Views: 795
Posted By GenoMax
Are you using 10x? If so take a look at:...

Are you using 10x? If so take a look at: https://kb.10xgenomics.com/hc/en-us/articles/115002022743-What-is-the-recommended-sequencing-depth-for-Single-Cell-3-and-5-Gene-Expression-libraries-
Forum: Bioinformatics 04-16-2020, 10:51 AM
Replies: 4
Views: 578
Posted By GenoMax
I see. Did you merge the data using `bbmerge`? If...

I see. Did you merge the data using `bbmerge`? If not can you try it instead of whichever program you used? I am not sure having Q-scores that go past even Illumina encoding make sense.
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