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Search: Posts Made By: GenoMax
Forum: Bioinformatics 04-02-2020, 11:51 AM
Replies: 19
Views: 411
Posted By GenoMax
I see. We don't use either. Thanks for that info....

I see. We don't use either. Thanks for that info.

In any case the Demux file seems to be in a different format. Again may be due to use of MiSeq reporter/BaseSpace.
Forum: Bioinformatics 04-02-2020, 11:28 AM
Replies: 19
Views: 411
Posted By GenoMax
Please come back and post when you hear from tech...

Please come back and post when you hear from tech support. I am curious to see the outcome of this as well.
Forum: Bioinformatics 04-02-2020, 11:03 AM
Replies: 19
Views: 411
Posted By GenoMax
I am afraid something has gone wrong with this...

I am afraid something has gone wrong with this run. Either specific index cycles failed (where you see the . ) or more likely (hate to say this) your libraries may have failed. Either scenario would...
Forum: Bioinformatics 04-02-2020, 10:53 AM
Replies: 19
Views: 411
Posted By GenoMax
Ah so your run was dual-indexed. I am puzzled as...

Ah so your run was dual-indexed. I am puzzled as to why your reads don't have any index sequence in fastq headers.

What do you see in DemuxSummaryF1L1.txt?

Scroll down the file until your see...
Forum: Bioinformatics 04-02-2020, 10:34 AM
Replies: 19
Views: 411
Posted By GenoMax
@mmhefny, Are you sure this run was set up...

@mmhefny,

Are you sure this run was set up to run a index cycle? This run header does not seem to make it look so.

@M02006:24:000000000-J397M:1:1101:21922:3716 2:N:0:0

Normally one should...
Forum: Bioinformatics 04-02-2020, 08:08 AM
Replies: 19
Views: 411
Posted By GenoMax
Are you able to use command line? If you are I...

Are you able to use command line? If you are I can suggest some options to look at those "Undetermined" files to see what may be going on.

If you are able to open them (on PC/Mac) post a small...
Forum: Bioinformatics 04-02-2020, 05:39 AM
Replies: 19
Views: 411
Posted By GenoMax
It won't be very useful to look at the...

It won't be very useful to look at the Samplesheet. If MiSeq accepted it at run time then it must have been in the correct format. If your samples did not demultiplex then it is very likely that you...
Forum: Bioinformatics 04-02-2020, 02:52 AM
Replies: 19
Views: 411
Posted By GenoMax
Sounds like you had a demultiplexing failure....

Sounds like you had a demultiplexing failure. Check your sample sheet one more time (easy mistake is to provide the indexes in rev-comp) and re-queue demultiplexing. You should use Illumina...
Forum: Bioinformatics 03-28-2020, 03:54 AM
Replies: 64
Views: 31,941
Posted By GenoMax
@Amanda: I will need to dig through some past...

@Amanda: I will need to dig through some past correspondence with Brian but I think he had recommended splitting first and then mapping to avoid the problem of having all references present in the...
Forum: RNA Sequencing 03-26-2020, 04:24 AM
Replies: 2
Views: 196
Posted By GenoMax
Rather then indeterminate, N signifies that a...

Rather then indeterminate, N signifies that a reliable base call is not possible at that location.

N's are also included to indicate locations where current sequencing technologies are unable to...
Forum: Bioinformatics 03-19-2020, 06:05 PM
Replies: 1
Views: 358
Posted By GenoMax
Listen to your IT recommendations. It is one...

Listen to your IT recommendations. It is one thing to have cores but if you don't have storage infrastructure to support the I/O needs then that will always be the bottleneck. When you run these...
Forum: RNA Sequencing 03-16-2020, 07:30 AM
Replies: 7
Views: 726
Posted By GenoMax
You should scan and trim the data before aligning...

You should scan and trim the data before aligning if there are substantial poly-G tails present.

You can find the sequence of human rDNA repeat here (http://www.ncbi.nlm.nih.gov/nuccore/U13369),...
Forum: Bioinformatics 03-10-2020, 04:13 AM
Replies: 244
Views: 96,215
Posted By GenoMax
@roselaw27: You can use `-F` option with...

@roselaw27: You can use `-F` option with fastq-dump to try and recreate fastq headers in original illumina format.
Forum: Bioinformatics 03-02-2020, 01:53 AM
Replies: 1
Views: 600
Posted By GenoMax
Cross-posted and answered on Biostars:...

Cross-posted and answered on Biostars: https://www.biostars.org/p/424091/
Forum: Illumina/Solexa 02-27-2020, 04:10 AM
Replies: 4
Views: 1,111
Posted By GenoMax
Since these systems have not been released as yet...

Since these systems have not been released as yet it is not surprising that the information is not yet available. Only thing publicly available seems to be this spec sheet...
Forum: Bioinformatics 02-22-2020, 03:26 AM
Replies: 1
Views: 690
Posted By GenoMax
Cross-posted on biostars:...

Cross-posted on biostars: https://www.biostars.org/p/423541/

I will keep answering there.
Forum: Bioinformatics 02-14-2020, 03:38 AM
Replies: 3
Views: 831
Posted By GenoMax
You are identifying changes w.r.t. a reference...

You are identifying changes w.r.t. a reference and then comparing those results to get the difference between your control and mutant results.
Forum: Bioinformatics 02-13-2020, 11:38 AM
Replies: 3
Views: 831
Posted By GenoMax
You need just step 1 from this tutorial ...

You need just step 1 from this tutorial (https://www.biostars.org/p/367960/) since you only want SNv.
Forum: Illumina/Solexa 02-06-2020, 06:25 AM
Replies: 2
Views: 572
Posted By GenoMax
While I don't have direct experience with MiniSeq...

While I don't have direct experience with MiniSeq it sounds like a problem with demultiplexing. Do you have an install of bcl2fastq available that you could use offline to do the demux again?
Forum: Sample Prep / Library Generation 02-06-2020, 04:12 AM
Replies: 21
Views: 6,084
Posted By GenoMax
Illumina did release a new version of RiboZero+...

Illumina did release a new version of RiboZero+ yesterday: https://www.illumina.com/products/by-type/accessory-products/ribo-zero-plus-rrna-depletion.html
Forum: Illumina/Solexa 02-04-2020, 03:28 PM
Replies: 5
Views: 747
Posted By GenoMax
Demultiplexing may fail, if your indexes are...

Demultiplexing may fail, if your indexes are non-standard and you provide standard indexes (but the run will not fail so don't worry). Edit the samplesheet and put the actual indexes you used. You...
Forum: Bioinformatics 02-04-2020, 06:00 AM
Replies: 2
Views: 434
Posted By GenoMax
Have you looked at this:...

Have you looked at this: http://seqanswers.com/forums/showthread.php?t=42552
Forum: General 02-03-2020, 04:24 PM
Replies: 1
Views: 827
Posted By GenoMax
Answered in this thread:...

Answered in this thread: http://seqanswers.com/forums/showthread.php?t=92819
Forum: Bioinformatics 02-03-2020, 04:23 PM
Replies: 4
Views: 540
Posted By GenoMax
There are databases e.g. SILVA...

There are databases e.g. SILVA (https://www.arb-silva.de/) that provide this information. NCBI (https://www.ncbi.nlm.nih.gov/refseq/targetedloci/16S_process/) also has a 16S microbial dataset.

As...
Forum: Bioinformatics 02-03-2020, 05:20 AM
Replies: 4
Views: 540
Posted By GenoMax
For analysis of 16S data you will want to use an...

For analysis of 16S data you will want to use an established pipeline such as Qiime (link (https://docs.qiime2.org/2019.10/)).
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