Forum: Bioinformatics
12-09-2021, 04:35 AM
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Replies: 703
Views: 271,781
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Forum: Bioinformatics
12-08-2021, 11:44 AM
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Replies: 703
Views: 271,781
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Forum: Bioinformatics
10-12-2021, 06:17 AM
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Replies: 4
Views: 2,902
Your reads have been processed in some manner...
Your reads have been processed in some manner (i.e., filtered by quality) so that R1 and R2 are no longer properly paired. For unprocessed reads, the number of R1 and R2 should be identical, and you...
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Forum: Bioinformatics
09-10-2021, 08:04 AM
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Replies: 703
Views: 271,781
"Exception in thread "main"...
"Exception in thread "main" java.lang.AssertionError: Attempting to output paired reads to different sam files."
Typically, BBMap tools keep paired reads together. You're attempting to write...
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Forum: Bioinformatics
08-25-2020, 06:01 AM
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Replies: 1
Views: 1,622
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, 11:20 AM
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Replies: 2
Views: 2,468
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Forum: Illumina/Solexa
08-07-2020, 05:59 AM
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Replies: 3
Views: 2,154
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, 11:11 AM
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Replies: 1
Views: 3,094
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Forum: Bioinformatics
02-04-2020, 06:38 AM
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Replies: 2
Views: 1,300
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Forum: Sample Prep / Library Generation
11-07-2019, 03:51 AM
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Replies: 2
Views: 2,498
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, 05:51 AM
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Replies: 12
Views: 5,548
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, 04:53 PM
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Replies: 11
Views: 17,308
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, 04:59 AM
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Replies: 2
Views: 1,512
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Forum: Sample Prep / Library Generation
12-14-2018, 05:22 AM
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Replies: 4
Views: 3,103
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Forum: Introductions
11-13-2018, 04:17 AM
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Replies: 2
Views: 2,572
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Forum: Bioinformatics
08-09-2018, 06:08 AM
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Replies: 703
Views: 271,781
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Forum: Sample Prep / Library Generation
07-30-2018, 04:43 PM
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Replies: 1
Views: 2,089
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, 09:32 AM
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Replies: 2
Views: 3,117
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, 01:03 PM
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Replies: 7
Views: 8,911
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Forum: Bioinformatics
03-15-2018, 06:48 AM
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Replies: 703
Views: 271,781
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Forum: Bioinformatics
02-28-2018, 05:07 AM
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Replies: 5
Views: 3,040
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, 08:34 AM
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Replies: 5
Views: 3,040
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Forum: Sample Prep / Library Generation
02-02-2018, 04:31 AM
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Replies: 2
Views: 1,683
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Forum: RNA Sequencing
11-08-2017, 06:28 AM
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Replies: 5
Views: 2,932
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Forum: Illumina/Solexa
11-01-2017, 05:13 AM
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Replies: 13
Views: 2,527
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