Forum: Illumina/Solexa
03-05-2021, 06:41 PM
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Replies: 7
Views: 270
That would be fine.
Edit: SNPSarus makes a...
That would be fine.
Edit: SNPSarus makes a good point below. If the gene density of your organism is similar then an equivalent reduction would be fine. Otherwise scale accordingly.
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Forum: Illumina/Solexa
03-05-2021, 04:13 PM
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Replies: 7
Views: 270
Generally for human samples (3 gb genome) one...
Generally for human samples (3 gb genome) one would want to target around 25-30 Million reads per sample. So use that as an approximation to calculate the number of reads you would need per sample.
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Forum: Illumina/Solexa
03-04-2021, 06:02 AM
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Replies: 2
Views: 220
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Forum: Illumina/Solexa
03-01-2021, 04:52 AM
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Replies: 1
Views: 229
You should be able to run MiSeq nano FC (~1 M...
You should be able to run MiSeq nano FC (~1 M clusters) to check the balance of libraries and most of all to verify that libraries have worked. We routinely do that for pools destined for NovaSeq.
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Forum: Illumina/Solexa
02-10-2021, 11:22 AM
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Replies: 2
Views: 629
It appears to be about 2x faster compared to...
It appears to be about 2x faster compared to bcl2fastq on identical datasets. It is producing different folder structure for result/log files (no more html reports) but plain csv so they should be...
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Forum: Bioinformatics
02-04-2021, 04:06 PM
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Replies: 7
Views: 3,426
BBMap suite programs try to auto detect memory...
BBMap suite programs try to auto detect memory available on your system. If they are not able to do that they will fall back to using a safe 2GB using the option mentioned "-Xmx2000m". This is Java...
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Forum: Bioinformatics
02-03-2021, 11:35 AM
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Replies: 39
Views: 33,945
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Forum: Bioinformatics
01-31-2021, 01:08 PM
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Replies: 1
Views: 691
If these are prokarotic genomes them Mauve...
If these are prokarotic genomes them Mauve (http://darlinglab.org/mauve/mauve.html) will work. If these are larger eukaryotic genomes them tools like Mugsy (http://mugsy.sourceforge.net/) or MUMMER4...
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Forum: Bioinformatics
01-26-2021, 04:53 AM
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Replies: 4
Views: 779
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Forum: Illumina/Solexa
01-25-2021, 09:20 AM
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Replies: 3
Views: 779
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Forum: Illumina/Solexa
01-25-2021, 03:27 AM
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Replies: 3
Views: 779
Why is your facility not doing the...
Why is your facility not doing the demultiplexing? This should be very simple for them to do.
It is normal to have a few reads at the beginning of the file to have some N's but are you saying...
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Forum: Bioinformatics
11-29-2020, 04:47 PM
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Replies: 1
Views: 756
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Forum: Illumina/Solexa
11-18-2020, 02:52 AM
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Replies: 4
Views: 753
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Forum: Illumina/Solexa
11-07-2020, 05:49 AM
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Replies: 1
Views: 1,034
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Forum: Bioinformatics
09-29-2020, 02:30 AM
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Replies: 2
Views: 1,189
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Forum: Bioinformatics
09-19-2020, 04:44 AM
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Replies: 5
Views: 1,420
Create a ticket...
Create a ticket (https://sourceforge.net/projects/bbmap/support) via BBMap's repo so Brian is aware of the problem.
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Forum: Bioinformatics
09-17-2020, 08:42 AM
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Replies: 5
Views: 1,420
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Forum: RNA Sequencing
09-15-2020, 06:16 PM
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Replies: 6
Views: 2,038
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Forum: General
09-15-2020, 03:02 AM
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Replies: 2
Views: 1,981
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Forum: RNA Sequencing
09-14-2020, 10:37 AM
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Replies: 6
Views: 2,038
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Forum: Bioinformatics
09-10-2020, 10:37 AM
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Replies: 5
Views: 1,420
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Forum: Bioinformatics
09-04-2020, 09:09 AM
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Replies: 2
Views: 1,932
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Forum: Illumina/Solexa
09-02-2020, 03:07 AM
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Replies: 8
Views: 3,536
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Forum: Bioinformatics
09-01-2020, 09:58 AM
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Replies: 4
Views: 1,012
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Forum: Bioinformatics
09-01-2020, 02:51 AM
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Replies: 4
Views: 1,012
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