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Search: Posts Made By: GenoMax
Forum: General Yesterday, 06:53 AM
Replies: 1
Views: 181
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: 251
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: 251
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: 323
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: 323
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: 319
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: 319
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: 319
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: 722
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: 722
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: 358
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: 358
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: 358
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: 426
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.
Forum: Bioinformatics 04-16-2020, 06:14 AM
Replies: 4
Views: 426
Posted By GenoMax
If this data is in Illumina encoding (Phred+64)...

If this data is in Illumina encoding (Phred+64) then you need to specify "qin=64". If you need the Q scores reformatted to sanger then "qout=33".
Forum: Bioinformatics 04-12-2020, 07:13 AM
Replies: 2
Views: 630
Posted By GenoMax
Is order of repositories in your ".condarc" file...

Is order of repositories in your ".condarc" file correct?


conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge


All packages...
Forum: Introductions 04-08-2020, 07:51 AM
Replies: 4
Views: 1,149
Posted By GenoMax
You could try kolabtree...

You could try kolabtree (https://www.kolabtree.com/). Strange site name. I am not affiliated with it in any way.

That said you should consider having someone on a monthly retainer. I assume...
Forum: Illumina/Solexa 04-06-2020, 11:50 AM
Replies: 2
Views: 960
Posted By GenoMax
Anecdotally we find MiSeq to be the best...

Anecdotally we find MiSeq to be the best sequencer for odd samples. You best bet is to sequence this library there. You can always a run a nano flowcell at a much reduced cost to test before you run...
Forum: Bioinformatics 04-06-2020, 03:12 AM
Replies: 131
Views: 66,814
Posted By GenoMax
If you have two separate sequencing runs you...

If you have two separate sequencing runs you can't "merge" the two reads since they are not sequencing the same fragment. Reason you can (in some cases) merge two reads R1/R2 to get a longer...
Forum: Bioinformatics 04-02-2020, 11:51 AM
Replies: 19
Views: 766
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: 766
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: 766
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: 766
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: 766
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: 766
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...
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