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Forum: Illumina/Solexa 03-09-2020, 02:27 PM
Replies: 7
Views: 2,106
Posted By SNPsaurus
I think the problem comes from Illumina errors...

I think the problem comes from Illumina errors not being perfectly random and that this bias is not being reflected in the quality scores. At 1 in a million there will be a higher background of...
Forum: Illumina/Solexa 03-05-2020, 11:35 AM
Replies: 7
Views: 2,106
Posted By SNPsaurus
Right, the barcoding does require a certain level...

Right, the barcoding does require a certain level of presence in the population otherwise one pool has it the other does not. 1 in a million still sounds too rare to be able to identify. Can you...
Forum: Bioinformatics 03-05-2020, 11:30 AM
Replies: 6
Views: 1,547
Posted By SNPsaurus
You used bbmerge already, so it sounds like you...

You used bbmerge already, so it sounds like you have bbtools installed.
reformat.sh in=read1,fq,gz in2=read2.fq.gz out=read1_fewer.fq.gz out2=read2_fewer.fq.gz reads=10000000
Forum: Bioinformatics 03-04-2020, 12:38 PM
Replies: 6
Views: 1,547
Posted By SNPsaurus
I would use bbtools reformat to set the number of...

I would use bbtools reformat to set the number of desired reads.
Forum: Illumina/Solexa 02-27-2020, 09:45 PM
Replies: 4
Views: 1,960
Posted By SNPsaurus
The Omics Omics blog by Keith Robison is a good...

The Omics Omics blog by Keith Robison is a good source of information about new systems, but he also wonders how many copies are in a cluster....
Forum: Illumina/Solexa 02-19-2020, 10:18 PM
Replies: 7
Views: 2,106
Posted By SNPsaurus
That's a pretty good idea! We published an...

That's a pretty good idea! We published an approach like that :-) https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2669-3

However, it would be hard to drive it down to 1 in 1...
Forum: Bioinformatics 02-09-2020, 07:28 PM
Replies: 6
Views: 1,547
Posted By SNPsaurus
Is your 18 Gb of Illumina data pure mtDNA or...

Is your 18 Gb of Illumina data pure mtDNA or mtDNA plus nuclear? If it is pure mtDNA then you probably have many thousand-fold coverage of the mitochondrial genome and you can reduce the number of...
Forum: Bioinformatics 01-30-2020, 03:26 PM
Replies: 2
Views: 1,072
Posted By SNPsaurus
I'd try a speedy assembler like BBtools...

I'd try a speedy assembler like BBtools tadpole.sh as a first pass just to see what a rough draft looks like. A slower assembler but one that should finish in a day is abyss-pe with the bloom filter...
Forum: Bioinformatics 01-09-2020, 10:45 PM
Replies: 2
Views: 1,204
Posted By SNPsaurus
I just tried your code on a test set with a...

I just tried your code on a test set with a random kmer in the 3rd read in bold

@NGSNJ-086:222:GW191226409th:1:1103:5556:31187 1:N:0:GAAGCGGCAC+CGGCTCTACT...
Forum: Bioinformatics 12-09-2019, 08:14 PM
Replies: 678
Views: 201,704
Posted By SNPsaurus
Did you try the suggested "Please manually set...

Did you try the suggested "Please manually set qin=33 or qin=64"?
Forum: Bioinformatics 11-27-2019, 09:25 PM
Replies: 3
Views: 4,312
Posted By SNPsaurus
Francesco, I didn't quite understand what you...

Francesco, I didn't quite understand what you have, but if you have a large merged vcf and want to reduce it to a specific region of the genome or only show polymorphic SNPs in your 4 samples then...
Forum: Bioinformatics 11-27-2019, 09:19 PM
Replies: 3
Views: 4,312
Posted By SNPsaurus
The merge vcf tool looks to link to a vcard...

The merge vcf tool looks to link to a vcard format merger, not the genomic one!
Forum: Bioinformatics 11-25-2019, 09:15 AM
Replies: 1
Views: 948
Posted By SNPsaurus
This isn't so helpful to solve the asked problem,...

This isn't so helpful to solve the asked problem, but PacBio HiFi reads might be a better choice since you can generate 15kb sequences at 1% or 0.1% error rates. They might more obviously segregate...
Forum: General 11-23-2019, 07:35 AM
Replies: 1
Views: 2,334
Posted By SNPsaurus
If you want to represent the Phred score as an...

If you want to represent the Phred score as an text character, then you need to use "letters". Look at the list of ASCII characters and what the first 32 represent...
Forum: Bioinformatics 11-20-2019, 04:43 PM
Replies: 5
Views: 2,321
Posted By SNPsaurus
Sorry, that's out of my area. Your IT support...

Sorry, that's out of my area. Your IT support might know it if it is a static IP, or have a way to look it up from the jack if it is assigned.
Forum: Bioinformatics 11-19-2019, 02:40 PM
Replies: 5
Views: 2,321
Posted By SNPsaurus
It depends on the installation. On a mac laptop,...

It depends on the installation. On a mac laptop, open your terminal and
ssh username@IP.address (with your username and your server's IP address) and then give your password. On a PC/chromebook get...
Forum: Bioinformatics 11-19-2019, 10:13 AM
Replies: 5
Views: 2,321
Posted By SNPsaurus
Can you login via ssh from another computer to...

Can you login via ssh from another computer to avoid the flickering?
Forum: De novo discovery 11-12-2019, 04:51 PM
Replies: 2
Views: 4,304
Posted By SNPsaurus
PacBio assemblies will have contig and scaffold...

PacBio assemblies will have contig and scaffold stats that are very close. I guess single-end Illumina or paired-end Illumina on short fragments would also be like that?
Forum: Illumina/Solexa 11-06-2019, 10:14 AM
Replies: 18
Views: 2,399
Posted By SNPsaurus
After seeing the updates it probably wouldn't...

After seeing the updates it probably wouldn't help much. Some library preps can have a high percentage of non-functional DNA fragments but a PCR amplicon should be pretty reliable. And if you are...
Forum: Illumina/Solexa 11-05-2019, 09:16 AM
Replies: 18
Views: 2,399
Posted By SNPsaurus
The $800 is very very low. Even twice that would...

The $800 is very very low. Even twice that would be on the low end at many service providers for 2x300 v3 MiSeq.

Have you compared Qubit numbers to qPCR to see if there is a mismatch in those...
Forum: Bioinformatics 10-09-2019, 09:34 AM
Replies: 3
Views: 1,178
Posted By SNPsaurus
You want to split the string on a "." delimiter...

You want to split the string on a "." delimiter and then keep the first two parts. Or use ".fastq.sam.bam" as a delimiter, I suppose!
...
Forum: Illumina/Solexa 10-09-2019, 09:29 AM
Replies: 2
Views: 1,596
Posted By SNPsaurus
Index hopping can produce that result. Are you...

Index hopping can produce that result. Are you using the index hopping blocking kit from Illumina? But either way, dual uniques are the way to go.
Forum: Pacific Biosciences 10-06-2019, 09:08 AM
Replies: 6
Views: 5,403
Posted By SNPsaurus
Oh my, that's a big one. How much memory is it...

Oh my, that's a big one. How much memory is it using?

If you just want a rough assembly, I would do wtdbg2 as you can get a sense of contig lengths without consensus generation. I've done flye...
Forum: Bioinformatics 10-04-2019, 09:59 AM
Replies: 1
Views: 1,395
Posted By SNPsaurus
That would require some scripting, I think....

That would require some scripting, I think. vcftools can filter for sites within a range of read depth, so you could:
extract one individual with vcftools --indv
find the mean depth with vcftools...
Forum: Pacific Biosciences 10-03-2019, 01:34 PM
Replies: 6
Views: 5,403
Posted By SNPsaurus
What kind of genome are you trying to assemble? I...

What kind of genome are you trying to assemble? I usually go with flye as a first pass (fast, memory efficient) and then Canu if flye underperforms (they seem to trade off which gives a better...
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