Forum: Epigenetics
08-14-2020, 12:31 AM
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Replies: 37
Views: 37,487
Hi Anton,
The methylation rate in Unknown...
Hi Anton,
The methylation rate in Unknown context is really only for your information, but as these calls cannot be assigned a specific context they are just discarded in the methylation...
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Forum: Epigenetics
07-13-2020, 10:00 AM
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Replies: 37
Views: 37,487
Hi Iraia,
I don't think you should start...
Hi Iraia,
I don't think you should start aligning the entire file until you know exactly what is the best way to do it. You are absolutely welcome to send me a few reads.
If you are on Linux or...
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Forum: Epigenetics
07-06-2020, 09:29 AM
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Replies: 37
Views: 37,487
Hi there,
The mm10 and GRCm38 genomes should...
Hi there,
The mm10 and GRCm38 genomes should be exactly the same sequence, there are only some minor differences (e.g. chromosomes are called chr1, chr2 and not 1, 2 etc, chrM instead of MT and so...
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Forum: Bioinformatics
01-31-2020, 05:00 AM
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Replies: 4
Views: 812
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Forum: Bioinformatics
01-31-2020, 01:54 AM
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Replies: 4
Views: 812
Hi Hedi,
Every alignment that is reported by...
Hi Hedi,
Every alignment that is reported by Bismark are unique hits (ambiguosly aligning reads are discarded, and not-aligning reads - well - don't align at all). So you can simply look at the...
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Forum: Epigenetics
09-24-2019, 03:51 AM
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Replies: 1
Views: 6,274
Dear Ali,
Thanks for your kind words, and...
Dear Ali,
Thanks for your kind words, and for your thoughtful questions. As you will see below, I will probably not be able to give you a satisfactory answer to all questions you raised, but I...
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Forum: Illumina/Solexa
09-13-2019, 06:52 AM
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Replies: 1
Views: 1,264
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Forum: Bioinformatics
06-02-2019, 09:12 AM
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Replies: 13
Views: 2,621
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Forum: Bioinformatics
05-29-2019, 01:43 AM
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Replies: 13
Views: 2,621
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Forum: Bioinformatics
05-28-2019, 05:00 AM
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Replies: 13
Views: 2,621
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Forum: Bioinformatics
05-28-2019, 03:02 AM
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Replies: 13
Views: 2,621
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Forum: Bioinformatics
01-18-2019, 02:24 AM
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Replies: 138
Views: 49,480
Trim Galore tries to identify read-through...
Trim Galore tries to identify read-through adapter contamination, which is the kind of contaminant that will prevent your sequences from aligning at all, or might even cause mis-alignments. For the...
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Forum: Bioinformatics
01-17-2019, 01:47 AM
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Replies: 138
Views: 49,480
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Forum: Bioinformatics
12-18-2018, 08:35 AM
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Replies: 3
Views: 6,142
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Forum: Bioinformatics
11-20-2018, 02:49 AM
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Replies: 1
Views: 843
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Forum: Bioinformatics
10-04-2018, 08:16 AM
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Replies: 648
Views: 191,300
Hi Amira,
The reason for this is the overlap...
Hi Amira,
The reason for this is the overlap detection, and -removal, in paired-end files. What this simply does is to detect when R1 and R2 start overlapping, and as soon as this is the case the...
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Forum: Bioinformatics
09-05-2018, 04:06 AM
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Replies: 648
Views: 191,300
Just generally, in order to get reads for both...
Just generally, in order to get reads for both the forward and reverse strands you need to have a fairly good sequencing depth and have a library with a good complexity. While your sample 1 has...
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Forum: Bioinformatics
09-04-2018, 07:59 AM
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Replies: 13
Views: 2,621
Sorry for the late reply but I was travelling....
Sorry for the late reply but I was travelling. And no I don't think a second trim is necessary, the 20bp is an arbitrary cutoff anyway because sequences shorter than that will typically not map...
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Forum: Bioinformatics
09-04-2018, 03:19 AM
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Replies: 648
Views: 191,300
Hi Daisy,
Were you expecting to see...
Hi Daisy,
Were you expecting to see imbalances in your library, i.e. was it some kind of target enrichment or (PCR) amplification library? Depending on what you expect from the library design you...
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Forum: Bioinformatics
08-14-2018, 04:03 AM
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Replies: 2
Views: 1,505
Hi Hedi,
No, I'm afraid you can’t say...
Hi Hedi,
No, I'm afraid you can’t say that. The numbers reported are the overall numbers of methylation calls performed for the entire run, and have nothing to do with the number of genomic...
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Forum: Bioinformatics
07-30-2018, 04:07 AM
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Replies: 6
Views: 1,397
Not quite. A 0.04 fold-coverage means that - on...
Not quite. A 0.04 fold-coverage means that - on average - each position in the genome was covered 0.04 times. A 4-fold would be, well, 4.
This value is obviously not so meaningful if you used only...
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Forum: Bioinformatics
07-30-2018, 03:13 AM
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Replies: 6
Views: 1,397
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Forum: Bioinformatics
07-27-2018, 02:40 AM
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Replies: 6
Views: 1,397
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Forum: Bioinformatics
07-26-2018, 04:07 AM
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Replies: 13
Views: 2,621
Hi Hedi86,
Thanks for providing the data. I...
Hi Hedi86,
Thanks for providing the data. I have now run a few preliminary tests, here is what I found (in no particular order):
- From the sequence composition plot, the data does not look...
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Forum: Bioinformatics
07-25-2018, 07:06 AM
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Replies: 13
Views: 2,621
Hi Hedi,
Could you email...
Hi Hedi,
Could you email (felix.krueger@babraham.ac.uk) some unprocessed reads, e.g. 200000, to me in .gz format? I could then take a look and report back to you with what I find.
Cheers, Felix
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