Forum: Bioinformatics
08-25-2020, 07:01 AM
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Replies: 1
Views: 944
The first error message indicates that your...
The first error message indicates that your reference genome is the culprit. Some versions contain 'N's that correspond to placeholders for the telomeric repeats. This causes reference indexing to...
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Forum: Bioinformatics
08-07-2020, 12:20 PM
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Replies: 2
Views: 1,341
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Forum: Illumina/Solexa
08-07-2020, 06:59 AM
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Replies: 3
Views: 1,519
Yes, you can perform asymmetric runs - it's...
Yes, you can perform asymmetric runs - it's routine for single-cell RNA-Seq. Quality will decline with read length, and (in our experience) drops to unacceptable levels when you exceed the...
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Forum: General
07-06-2020, 12:11 PM
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Replies: 1
Views: 2,259
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Forum: Bioinformatics
02-04-2020, 07:38 AM
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Replies: 2
Views: 760
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Forum: Sample Prep / Library Generation
11-07-2019, 04:51 AM
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Replies: 2
Views: 1,551
The simplest way to isolate the problem is to...
The simplest way to isolate the problem is to have new facility sequence the old (high quality) sample - if the data are good, it's not the facility. Alternatively, prepare your next sample with both...
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Forum: Illumina/Solexa
05-25-2019, 06:51 AM
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Replies: 12
Views: 3,891
Our small core lab likes the flexibility of the...
Our small core lab likes the flexibility of the 2500, especially Rapid mode for small numbers of samples/unusual run requests. Replacing that functionality would require two machines (although we are...
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Forum: General
01-03-2019, 05:53 PM
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Replies: 11
Views: 16,066
Use BEDtools 'genomecov'...
Use BEDtools 'genomecov' (https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html) command with '-d' flag to obtain per-base depth of coverage.
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Forum: Bioinformatics
01-02-2019, 05:59 AM
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Replies: 2
Views: 1,103
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Forum: Sample Prep / Library Generation
12-14-2018, 06:22 AM
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Replies: 4
Views: 2,160
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Forum: Introductions
11-13-2018, 05:17 AM
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Replies: 2
Views: 2,077
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Forum: Bioinformatics
08-09-2018, 07:08 AM
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Replies: 678
Views: 214,469
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Forum: Sample Prep / Library Generation
07-30-2018, 05:43 PM
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Replies: 1
Views: 1,686
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...
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Forum: Bioinformatics
07-24-2018, 10:32 AM
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Replies: 2
Views: 2,279
Explanation here...
Explanation here (https://academic.oup.com/bioinformatics/article/29/4/444/200320) (see section 2.3).
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Forum: Service Providers
04-04-2018, 02:03 PM
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Replies: 7
Views: 5,739
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Forum: Bioinformatics
03-15-2018, 07:48 AM
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Replies: 678
Views: 214,469
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Forum: Bioinformatics
02-28-2018, 06:07 AM
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Replies: 5
Views: 2,433
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...
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Forum: Bioinformatics
02-27-2018, 09:34 AM
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Replies: 5
Views: 2,433
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Forum: Sample Prep / Library Generation
02-02-2018, 05:31 AM
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Replies: 2
Views: 1,378
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Forum: RNA Sequencing
11-08-2017, 07:28 AM
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Replies: 5
Views: 2,493
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Forum: Illumina/Solexa
11-01-2017, 06:13 AM
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Replies: 13
Views: 2,092
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Forum: Illumina/Solexa
10-31-2017, 05:14 AM
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Replies: 13
Views: 2,092
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...
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Forum: Illumina/Solexa
09-26-2017, 01:14 PM
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Replies: 8
Views: 8,292
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Forum: Bioinformatics
07-31-2017, 08:23 AM
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Replies: 1
Views: 1,787
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...
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Forum: Illumina/Solexa
07-27-2017, 07:53 AM
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Replies: 13
Views: 3,263
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...
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