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Forum: Bioinformatics 03-20-2019, 09:23 AM
Replies: 6
Views: 218
Posted By SNPsaurus
I think luc is correct. You can inspect the bam...

I think luc is correct. You can inspect the bam file to see if the paired reads map to the same location. You can also run bbmerge and see if the two reads overlap and what percent of the library...
Forum: RNA Sequencing 02-11-2019, 08:47 PM
Replies: 4
Views: 433
Posted By SNPsaurus
This paper...

This paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015939/ shows >30% chloroplast-mapped reads in rRNA depleted total RNA prepared from seedlings. Your 70% is high, but a leaf might have more...
Forum: Bioinformatics 02-03-2019, 04:56 PM
Replies: 28
Views: 8,634
Posted By SNPsaurus
kcritap, are you trying to make sure that the...

kcritap, are you trying to make sure that the paired-end reads are kept as pairs? I would use bbduk from bbtools for trimming by quality and adapter removal.

bbduk.sh in=R1.fq in2=R2.fq ...
Forum: Bioinformatics 01-30-2019, 02:20 PM
Replies: 32
Views: 19,270
Posted By SNPsaurus
pepe84, do you provide a path to the file? Please...

pepe84, do you provide a path to the file? Please copy your command as tried, and then copy the error message.
Forum: Pacific Biosciences 01-26-2019, 02:38 PM
Replies: 6
Views: 1,188
Posted By SNPsaurus
We polish with arrow and just list one of the...

We polish with arrow and just list one of the outputs as fastq "-o sample_consensus.fastq" and it generates a fastq file with a consensus for each contig and the quality score. You might check if...
Forum: Bioinformatics 01-19-2019, 09:22 PM
Replies: 327
Views: 99,006
Posted By SNPsaurus
What's in your /bbmap/current/ directory? I have...

What's in your /bbmap/current/ directory? I have /bbmap/current/jgi/BBDukF.class
Forum: General 01-11-2019, 10:30 AM
Replies: 4
Views: 897
Posted By SNPsaurus
What kind of organisms were you genotyping. Some...

What kind of organisms were you genotyping. Some samples we do, like small insects, can have significant bacterial contamination due to the microbiome of the organism. Other kinds of samples, like...
Forum: Bioinformatics 01-10-2019, 06:32 AM
Replies: 2
Views: 617
Posted By SNPsaurus
You can filter your vcf for variants that fit...

You can filter your vcf for variants that fit your minor allele threshold with vcftools https://vcftools.github.io/man_latest.html

From the docs:
--non-ref-af <float>
--max-non-ref-af <float> ...
Forum: Vendor Forum 01-09-2019, 03:03 PM
Replies: 2
Views: 587
Posted By SNPsaurus
Yes, Sequel. I don't think we could bring the...

Yes, Sequel. I don't think we could bring the costs down enough with RSII.
Forum: Vendor Forum 01-09-2019, 12:26 PM
Replies: 2
Views: 587
Posted By SNPsaurus
PacBio microbial assembly service

With the new longer reads and higher output from PacBio we can pass the lower costs for de novo PacBio microbial sequencing along to you. Full service extraction, library prep and assembly/annotation...
Forum: Pacific Biosciences 01-08-2019, 08:08 PM
Replies: 5
Views: 962
Posted By SNPsaurus
I think the confusion is that they are calling...

I think the confusion is that they are calling all the contigs except for the largest "plasmid" which would be premature to do so without other evidence, especially if they are called as...
Forum: Bioinformatics 12-11-2018, 08:15 PM
Replies: 1
Views: 396
Posted By SNPsaurus
The bbtools program shred.sh will break a...

The bbtools program shred.sh will break a reference into chunks which can then be used for alignment. I'm not totally sure that is what you are looking for but it is my best bet!
Forum: Illumina/Solexa 11-29-2018, 07:49 PM
Replies: 3
Views: 878
Posted By SNPsaurus
SeqWell has some kits for high multiplexing.

SeqWell has some kits for high multiplexing.
Forum: Bioinformatics 11-27-2018, 08:32 PM
Replies: 2
Views: 464
Posted By SNPsaurus
It looks like the library fragment length was...

It looks like the library fragment length was short, so that many reads have an adapter trimmed off and (I imagine) many of the read 2s completely overlap the R1. What did the library fragment size...
Forum: Bioinformatics 09-25-2018, 09:47 AM
Replies: 665
Views: 150,996
Posted By SNPsaurus
Have you trimmed adapters away from the reads...

Have you trimmed adapters away from the reads (short fragments will create reads that are part genomic and part adapter and may not map). You could use the related BBmap tool sendsketch to get a...
Forum: General 09-12-2018, 08:03 PM
Replies: 1
Views: 1,612
Posted By SNPsaurus
RNA-Seq may use 10-30 million reads in an...

RNA-Seq may use 10-30 million reads in an experiment for expression profiling. SAGE would collect 10-50 thousand SAGE tags or so for a profile?
Forum: Bioinformatics 08-24-2018, 11:47 AM
Replies: 10
Views: 983
Posted By SNPsaurus
I'm not sure what is being measured by the...

I'm not sure what is being measured by the duplication level...I thought you were marking PCR duplicates.

If you have 1 million EcoRI sites, then I'd pick the best 15 samples (high alignment rate,...
Forum: Bioinformatics 08-24-2018, 11:09 AM
Replies: 10
Views: 983
Posted By SNPsaurus
You can't think about coverage that way with...

You can't think about coverage that way with RAD-Seq. You know that coverage will be zero across most of the genome, but then you will get high read depth at the RAD loci at the EcoRI sites. So I...
Forum: Bioinformatics 08-24-2018, 10:40 AM
Replies: 10
Views: 983
Posted By SNPsaurus
I think the problem is that you are sampling...

I think the problem is that you are sampling 500,000 sites which turns into 1 million RAD tags possible (each cut site has two tags that are sequenced) with an average of 500,000 reads per sample. So...
Forum: Bioinformatics 08-24-2018, 09:44 AM
Replies: 10
Views: 983
Posted By SNPsaurus
Was this regular RAD-Seq or ddRAD? There are...

Was this regular RAD-Seq or ddRAD? There are probably 500,000 EcoRI sites in a 2 Gb genome, so if you had 48 samples and 25 million reads even with perfect data you would get a read per site unless...
Forum: Bioinformatics 08-23-2018, 09:52 PM
Replies: 10
Views: 983
Posted By SNPsaurus
You have to be a little careful thinking about...

You have to be a little careful thinking about read coverage with RAD data...after all, it is meant to sample the genome at a small number of loci. So a "good" RAD sample might get 20X read depth at...
Forum: Genomic Resequencing 08-16-2018, 08:55 PM
Replies: 2
Views: 1,599
Posted By SNPsaurus
I haven't seen that error before. Were both bam...

I haven't seen that error before. Were both bam files sorted? Can you make a vcf file for each sample?
Forum: Bioinformatics 07-25-2018, 03:03 PM
Replies: 2
Views: 623
Posted By SNPsaurus
A phylip file should have actual DNA sequence for...

A phylip file should have actual DNA sequence for each sample, shouldn't it?
http://scikit-bio.org/docs/0.2.3/generated/skbio.io.phylip.html
Forum: Pacific Biosciences 07-04-2018, 11:10 AM
Replies: 2
Views: 1,905
Posted By SNPsaurus
As nucacidhunter says, while there is worry that...

As nucacidhunter says, while there is worry that multi-copy plasmids will overwhelm a sample, in practice plasmids can be under-represented. In the below examples, the plasmids are part of the...
Forum: Vendor Forum 06-28-2018, 09:16 AM
Replies: 0
Views: 1,382
Posted By SNPsaurus
SNPsaurus offers Illumina bacterial genome sequencing service

SNPsaurus is now offering Illumina PE 150 sequencing of bacterial genomes: library prep, sequencing to 60X read depth, assembly, annotation, and alignment to a reference with variant...
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