SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 498
Search took 0.03 seconds.
Search: Posts Made By: HESmith
Forum: Bioinformatics 08-09-2018, 06:08 AM
Replies: 651
Views: 134,278
Posted By HESmith
@JenBarb see this thread...

@JenBarb see this thread (https://www.biostars.org/p/297273/#297277) in Biostars.
Forum: Sample Prep / Library Generation 07-30-2018, 04:43 PM
Replies: 1
Views: 529
Posted By HESmith
Yes, adapter dimers can anneal to...

Yes, adapter dimers can anneal to insert-containing molecules via the adapter ends. The simplest solution is to perform one new round of PCR using ~1/2 (or less, depending upon the amount) of the...
Forum: Bioinformatics 07-24-2018, 09:32 AM
Replies: 2
Views: 399
Posted By HESmith
Explanation here...

Explanation here (https://academic.oup.com/bioinformatics/article/29/4/444/200320) (see section 2.3).
Forum: Service Providers 04-04-2018, 01:03 PM
Replies: 7
Views: 1,049
Posted By HESmith
https://genohub.com

https://genohub.com
Forum: Bioinformatics 03-15-2018, 06:48 AM
Replies: 651
Views: 134,278
Posted By HESmith
You can try the reformat.sh command per @GenoMax...

You can try the reformat.sh command per @GenoMax but with 'sam=1.3' flag. That worked for me with a different variant caller (FreeBayes).
Forum: Bioinformatics 02-28-2018, 05:07 AM
Replies: 5
Views: 783
Posted By HESmith
From the manual...

From the manual (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/dedupe-guide/): "Pair Limitations: Dedupe supports paired reads, but it was not really designed for them. When...
Forum: Bioinformatics 02-27-2018, 08:34 AM
Replies: 5
Views: 783
Posted By HESmith
Remove the spaces after the equals (=) signs and...

Remove the spaces after the equals (=) signs and try again.
Forum: Sample Prep / Library Generation 02-02-2018, 04:31 AM
Replies: 2
Views: 908
Posted By HESmith
Expression profiles can change in minutes, so I'd...

Expression profiles can change in minutes, so I'd recommend adding a stabilization component (e.g., Qiagen's RNAprotect) immediately after collection. At that point, the samples would be stable for...
Forum: RNA Sequencing 11-08-2017, 06:28 AM
Replies: 5
Views: 1,435
Posted By HESmith
The band is adaptor dimers. They form clusters....

The band is adaptor dimers. They form clusters. Use gel or bead purification to remove.
Forum: Illumina/Solexa 11-01-2017, 05:13 AM
Replies: 13
Views: 1,265
Posted By HESmith
Short templates/adapter dimers produce a drop-off...

Short templates/adapter dimers produce a drop-off in signal intensity, which @ATGCT doesn't observe (first thumbnail). And adapter dimers produce a diagnostic spiky signal, also not observed.
Forum: Illumina/Solexa 10-31-2017, 04:14 AM
Replies: 13
Views: 1,265
Posted By HESmith
The run is significantly over-clustered, as...

The run is significantly over-clustered, as indicated by the low PF (only 68%; should be mid-80s to mid-90s) in combination with the high error rate (4.4%; should be <1%). Quantify your libraries by...
Forum: Illumina/Solexa 09-26-2017, 12:14 PM
Replies: 5
Views: 1,461
Posted By HESmith
Read 1 begins with the RT primer. It contains the...

Read 1 begins with the RT primer. It contains the cell barcode, UMI, and oligo(dT), which primes 1st strand synthesis from the mRNA's poly(A) tail. Until you get past the poly(A), which can be long,...
Forum: Bioinformatics 07-31-2017, 07:23 AM
Replies: 1
Views: 606
Posted By HESmith
Adapter ligation is a concentration-dependent...

Adapter ligation is a concentration-dependent reaction. If enrichment is performed first, then the amount of one of the reactants (fragments) becomes low, which reduces the efficiency of the reaction...
Forum: Illumina/Solexa 07-27-2017, 06:53 AM
Replies: 13
Views: 1,505
Posted By HESmith
Yes, the longer oligos are more expensive. But...

Yes, the longer oligos are more expensive. But with dual indexing, 20 primers can accommodate 100 samples.

One more point to consider: PCR-free ligation prep requires a substantial amount (1-2...
Forum: Illumina/Solexa 07-27-2017, 06:15 AM
Replies: 13
Views: 1,505
Posted By HESmith
Ligation is always less efficient than...

Ligation is always less efficient than incorporating the adapter ends directly into your amplicon primers. Is there a reason NOT to use the following type of primer?

adapter end - index - random...
Forum: Illumina/Solexa 07-26-2017, 11:30 AM
Replies: 13
Views: 1,505
Posted By HESmith
I was wondering how you'd generate amplicons w/o...

I was wondering how you'd generate amplicons w/o PCR, but see that one round is acceptable. You can incorporate the sequencing adaptor ends into your target sequence primers, with random k-mers...
Forum: Bioinformatics 06-14-2017, 11:44 AM
Replies: 3
Views: 558
Posted By HESmith
It's not actually VCard format. It's just that...

It's not actually VCard format. It's just that VCard uses the same file extension (.vcf) as VCF, and your computer is configured to read the former by default. Open the VCF in a flat text editor and...
Forum: Bioinformatics 06-07-2017, 07:05 AM
Replies: 15
Views: 1,192
Posted By HESmith
Try BBMap's 'covstats' command - I think it...

Try BBMap's 'covstats' command - I think it provides a summary of coverage.
Forum: Bioinformatics 06-07-2017, 06:49 AM
Replies: 15
Views: 1,192
Posted By HESmith
You can determine how much of your genome is...

You can determine how much of your genome is covered, and at what read depth, using BEDTools 'genomecov' command (see here (http://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html) for...
Forum: Bioinformatics 05-31-2017, 09:18 AM
Replies: 651
Views: 134,278
Posted By HESmith
Not trying to be a jerk, but have you tried...

Not trying to be a jerk, but have you tried variant calling with the test data that are included with the software? Success would eliminate installation and command errors as the source of your...
Forum: Bioinformatics 05-31-2017, 09:04 AM
Replies: 651
Views: 134,278
Posted By HESmith
@jweger1988, what tools have you tried for VCF...

@jweger1988, what tools have you tried for VCF annotation and what problems have you encountered?
Forum: Bioinformatics 05-18-2017, 02:35 PM
Replies: 12
Views: 1,336
Posted By HESmith
IIRC, your previous posts about this topic were...

IIRC, your previous posts about this topic were deleted as inappropriate to the forum (and that hasn't changed).
Forum: Bioinformatics 03-11-2017, 03:48 PM
Replies: 2
Views: 697
Posted By HESmith
It has nothing to do with bridge amplification....

It has nothing to do with bridge amplification. WGS is whole-genome sequencing. The rRNA cluster is ~4500bp long, and a typical microbial genome is ~1000X as long. So only 1/1000 reads contain rRNA...
Forum: Pacific Biosciences 02-10-2017, 06:22 AM
Replies: 7
Views: 1,298
Posted By HESmith
1) What is the organism that you're studying? And...

1) What is the organism that you're studying? And are there any related genomes that might be useful for comparison?

2) Is there any possibility that the sample might be...
Forum: Bioinformatics 01-20-2017, 10:31 AM
Replies: 3
Views: 1,261
Posted By HESmith
There's a known incompatibility between FreeBayes...

There's a known incompatibility between FreeBayes and the CIGAR format of SAM/BAM v1.4, which results in no indel calls. If that's true for your FreeBayes VCF, reformat your alignment to v1.3 and...
Showing results 1 to 25 of 498

 


All times are GMT -8. The time now is 07:11 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO