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Forum: Bioinformatics 01-24-2019, 01:01 PM
Replies: 1
Views: 542
Posted By atpoint
Why don't you subsample your existing data to...

Why don't you subsample your existing data to 20mio reads and see if the results are good enough for what you want to do with them?
Forum: Sample Prep / Library Generation 01-24-2019, 12:56 PM
Replies: 10
Views: 3,321
Posted By atpoint
The original ATAC-seq protocol is very robust,...

The original ATAC-seq protocol is very robust, and if you do it properly for human or murine cells you'll see the banding pattern. All these modifications in the newer protocols might improve the...
Forum: Sample Prep / Library Generation 12-12-2018, 02:26 AM
Replies: 8
Views: 1,990
Posted By atpoint
Yes, this is most likely overtagmentated. It is...

Yes, this is most likely overtagmentated. It is also too much heat. ATAC-seq works at 37C for 30' with larger genomes like human and mouse. Worm genomes are much smaller, and therefore you might...
Forum: Sample Prep / Library Generation 12-12-2018, 12:03 AM
Replies: 8
Views: 1,990
Posted By atpoint
Hmm, you have a peak as expected at 180bp and...

Hmm, you have a peak as expected at 180bp and something that can be somekind of nucleosomal peak, but it indeed looks strange. Clearly not as expected. We did ATAC-seq in quiet a number of different...
Forum: Bioinformatics 12-11-2018, 09:39 AM
Replies: 1
Views: 465
Posted By atpoint
Cross-posted on Biostars...

Cross-posted on Biostars (https://www.biostars.org/p/353967/)
Forum: Sample Prep / Library Generation 12-11-2018, 07:34 AM
Replies: 8
Views: 1,990
Posted By atpoint
The two bioanalyzer pictures from OP actually...

The two bioanalyzer pictures from OP actually look OK to me, clear nucleosomal periodicity. Note that the peak at 180bp is not the mono-nucleosomal but the nucleosome-free peak. From the 180bp, you...
Forum: Bioinformatics 09-12-2018, 05:50 AM
Replies: 3
Views: 1,486
Posted By atpoint
The read should be soft-clipped. Use BWA mem for...

The read should be soft-clipped. Use BWA mem for alignment. Soft-clipping of reads is the basis of structural variant detection by many SV tools.
Forum: Bioinformatics 07-11-2018, 01:37 PM
Replies: 3
Views: 1,486
Posted By atpoint
You could make an alternative genome by masking...

You could make an alternative genome by masking the exons of geneA in the fasta (so adding N instead of the actual sequence), and then add the transgene sequence as an extra chromosome.
Forum: Illumina/Solexa 02-28-2018, 09:00 AM
Replies: 2
Views: 1,409
Posted By atpoint
Recommendation 150nt single-end vs 2x75nt paired-end

We are in the planning phase for an experiment that requires sequencing of a DNA pool of length about 140bp. It is crucial that the entire fragment is sequenced. Platform will be Nextseq500 or MiSeq,...
Forum: Bioinformatics 09-14-2017, 02:59 PM
Replies: 35
Views: 22,747
Posted By atpoint
I had the same error message using...

I had the same error message using processSomatic. It turned out to be a problem with the locate, which was non-UTF-8, see here on Biostars (https://www.biostars.org/p/272697/). Add export...
Forum: Bioinformatics 09-08-2016, 11:46 AM
Replies: 3
Views: 1,264
Posted By atpoint
Yes, on Illumina systems paired-end is basically...

Yes, on Illumina systems paired-end is basically an optional extension of single-end sequencing. Lets say you have a Nextseq platform and a kit for 150 cycles (means reagents to make 150 basecalls...
Forum: Bioinformatics 09-07-2016, 12:48 PM
Replies: 1
Views: 3,324
Posted By atpoint
- the total number of reads depends on the...

- the total number of reads depends on the platform you sequence on. on a miseq it should be about 25mio per flowcell, on a nextseq500 it can be up to 400mio. instead of total read numbers, better...
Forum: Bioinformatics 09-07-2016, 12:31 PM
Replies: 1
Views: 1,687
Posted By atpoint
The most straight-forward way would be to check...

The most straight-forward way would be to check the literature if there are ChIP-seq data available for the specific histone marks in your cell type AND! for the conditions you kept them.

If so,...
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