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Forum: Bioinformatics 10-09-2019, 09:34 AM
Replies: 3
Views: 254
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: 250
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: 3
Views: 397
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: 212
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: 3
Views: 397
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...
Forum: Bioinformatics 09-12-2019, 08:21 AM
Replies: 5
Views: 696
Posted By SNPsaurus
So this has 2 reads of the reference, but...

So this has 2 reads of the reference, but converts to a no call? Do other loci with only reads get called? There may be a firm threshold for needing >2 reads to support a call. GQ is 0, so that means...
Forum: General 09-12-2019, 08:11 AM
Replies: 14
Views: 1,251
Posted By SNPsaurus
You should do the entire command as Genomax...

You should do the entire command as Genomax listed (with a change, I think, I'll mention below):

for i in *.bam; do reformat.sh in=${i}.bam out=${i}.fa; done

The first part (for i in *.bam)...
Forum: General 09-11-2019, 10:58 AM
Replies: 14
Views: 1,251
Posted By SNPsaurus
Can you copy what you did as a command and paste...

Can you copy what you did as a command and paste it here, and then list the directory as well and paste a few filenames as well? It looks like it didn't find any bam files. Are there files ending in...
Forum: Bioinformatics 09-11-2019, 10:53 AM
Replies: 5
Views: 696
Posted By SNPsaurus
What is the output? A vcf file will typically...

What is the output? A vcf file will typically give the genotype call and then report on read depth, allele depth, genotype probabilities and quality scores for the call, mapping, and sequences. Can...
Forum: Bioinformatics 09-10-2019, 09:56 PM
Replies: 5
Views: 696
Posted By SNPsaurus
I like breseq...

I like breseq http://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing because it shows the evidence for each variant call and highlights regions of no coverage as well.
Forum: Bioinformatics 09-09-2019, 08:25 PM
Replies: 4
Views: 1,100
Posted By SNPsaurus
That had exactly the kind of language nitpicking...

That had exactly the kind of language nitpicking I was hoping to see!
Forum: Bioinformatics 09-06-2019, 09:16 PM
Replies: 4
Views: 1,100
Posted By SNPsaurus
I thought these papers were really interesting...

I thought these papers were really interesting perspectives on a difficult subject. Did you get people commenting on how you could have optimized their favorite language a bit more?
Forum: De novo discovery 08-14-2019, 06:31 AM
Replies: 7
Views: 1,236
Posted By SNPsaurus
Have you thought about using PacBio for long...

Have you thought about using PacBio for long amplicons instead of tagmenting and trying to re-assemble? Each amplicon could get multiple polymerase passes for a high-quality consensus, and be...
Forum: Bioinformatics 08-04-2019, 11:24 AM
Replies: 4
Views: 830
Posted By SNPsaurus
Are these proteins DNA-binding proteins, or are...

Are these proteins DNA-binding proteins, or are you wanting to find which DNA-binding proteins bind to the gene region of these proteins?
Forum: General 08-02-2019, 03:18 PM
Replies: 6
Views: 1,019
Posted By SNPsaurus
Those are all super cool, but I think the root of...

Those are all super cool, but I think the root of the problem is that sequencers are multiple-fold more complex than any of the other devices. A centrifuge spins fast, PCR heats and cools, but...
Forum: Bioinformatics 07-12-2019, 01:56 PM
Replies: 10
Views: 1,176
Posted By SNPsaurus
Our local facility offers 2x300 v3 MiSeq runs...

Our local facility offers 2x300 v3 MiSeq runs with 25 million reads and a 2x150 v2 run with 15 million reads. If I didn't need the extra 10 million reads, I might be tempted to just do 2x150 and...
Forum: Bioinformatics 07-12-2019, 09:37 AM
Replies: 10
Views: 1,176
Posted By SNPsaurus
I'm curious why you would select 2x300 for a 290...

I'm curious why you would select 2x300 for a 290 bp amplicon. Did you want to merge the paired reads for extra-high quality sequence?
Forum: Sample Prep / Library Generation 06-24-2019, 12:38 PM
Replies: 4
Views: 920
Posted By SNPsaurus
If they loaded PhiX at 5% but the library was...

If they loaded PhiX at 5% but the library was mis-estimated and actually much higher, then the actual PhiX could be lower, leading to poor quality scores.

Are you sequencing just one of the cut...
Forum: Sample Prep / Library Generation 06-19-2019, 12:00 PM
Replies: 4
Views: 920
Posted By SNPsaurus
Did the facility add extra PhiX to help the...

Did the facility add extra PhiX to help the basecalling in the low-complexity region of the cut site? What is the cut site?

It does seem like two issues. If you are getting lots of off-target...
Forum: Illumina/Solexa 06-08-2019, 09:27 PM
Replies: 2
Views: 977
Posted By SNPsaurus
I think most academic cores run the cheaper high...

I think most academic cores run the cheaper high output with 8 lanes rather than the fast and expensive rapid run mode and make users wait for a run of the appropriate type to fill up. Academic users...
Forum: General 06-05-2019, 10:04 PM
Replies: 1
Views: 1,402
Posted By SNPsaurus
Circulomics (makers of the HMW kit) has...

Circulomics (makers of the HMW kit) has customized the protocol for a particular species and sent back DNA. You might try them, although I don't know if they rush for a time crunch.

Have you...
Forum: Vendor Forum 05-31-2019, 12:14 PM
Replies: 0
Views: 1,018
Posted By SNPsaurus
PacBio Sequel II services

We think the PacBio Sequel II should force a giant change in how people approach routine sequencing work. In the past, the usual progression was to do the bulk of sequencing with Illumina short...
Forum: Sample Prep / Library Generation 05-23-2019, 11:11 AM
Replies: 4
Views: 819
Posted By SNPsaurus
I see, that makes sense for amplified mtDNA. ...

I see, that makes sense for amplified mtDNA.

You can combine the Nextera Flex and Nextera XT barcode sets for Nextera Flex preps. We do that for increased multiplexing.
Forum: Sample Prep / Library Generation 05-22-2019, 12:47 PM
Replies: 4
Views: 819
Posted By SNPsaurus
Can you multiplex that much on a Miseq and get...

Can you multiplex that much on a Miseq and get enough reads per sample to reconstruct the mitogenome? I guess if the nuclear genome isn't large then a reasonable fraction of reads will go to the...
Forum: Bioinformatics 05-21-2019, 01:13 PM
Replies: 2
Views: 648
Posted By SNPsaurus
wtdbg2 will overlap long reads and then...

wtdbg2 will overlap long reads and then correct/consensus as a separate step (I know this doesn't help getting Canu to do it that way, just following up on colindaven's comment).

Canu corrects...
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