Forum: Bioinformatics
12-24-2017, 12:09 PM
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Replies: 1
Views: 584
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Forum: Bioinformatics
11-28-2017, 05:55 AM
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Replies: 7
Views: 769
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Forum: Bioinformatics
11-28-2017, 12:46 AM
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Replies: 7
Views: 769
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Forum: Bioinformatics
11-22-2017, 04:26 AM
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Replies: 7
Views: 769
Hi Tsutsui,
In a case like yours Read 1...
Hi Tsutsui,
In a case like yours Read 1 seems to be absolutely fine, and your library is directional, so that looks all fine. If I had to guess what the reason for the low mapping efficiency in PE...
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Forum: Bioinformatics
10-22-2017, 01:11 AM
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Replies: 641
Views: 143,019
Hi Alan,
Thanks for making the files...
Hi Alan,
Thanks for making the files available. I have just tried to run your files with the following command line:
bismark2bedGraph --dir output_dir -o test --scaffold *G10G06*
And it...
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Forum: Bioinformatics
10-20-2017, 07:05 AM
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Replies: 641
Views: 143,019
Hi there,
Could you please update to the...
Hi there,
Could you please update to the latest version (0.19.0; https://github.com/FelixKrueger/Bismark/releases) to see if the problem is still there? If you are still seeing the same problem...
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Forum: Bioinformatics
10-20-2017, 04:09 AM
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Replies: 2
Views: 424
Hi Heidi86,
I think the answer to your...
Hi Heidi86,
I think the answer to your question is fairly simple: Bismark coverage files or the CpG methylation call files contain methylation data (as single-base calls), while SAM, BAM or sorted...
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Forum: Bioinformatics
10-04-2017, 04:39 AM
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Replies: 641
Views: 143,019
Hi Amira,
Your understanding is now spot-on!...
Hi Amira,
Your understanding is now spot-on! For the last point: For paired-end reads we always use the sum of the alignment scores (AS) and sum of the next best alignment scores (XS) of both...
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Forum: Bioinformatics
10-03-2017, 01:51 AM
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Replies: 641
Views: 143,019
Hi Amira,
I think that reads that produce...
Hi Amira,
I think that reads that produce more that one valid alignment should be reported based on Bowtie2 default mode (not all alignments, only one). How does having the same number of lowest...
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Forum: Sample Prep / Library Generation
08-10-2017, 01:51 AM
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Replies: 3
Views: 727
Hi aleichter,
I'd be happy to take at one...
Hi aleichter,
I'd be happy to take at one of the samples to see if I can find any of the typical suspects in the data. Emailing of a subset of say 500K sequences (gzipped) is typically sufficient...
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Forum: Bioinformatics
08-08-2017, 02:53 AM
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Replies: 641
Views: 143,019
We tend to use SeqMonk for this purpose...
We tend to use SeqMonk for this purpose (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). It is a very fast and powerful genome viewer and quantitation tool. Some examples can be found...
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Forum: Bioinformatics
07-28-2017, 12:58 AM
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Replies: 641
Views: 143,019
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Forum: Bioinformatics
06-29-2017, 01:43 AM
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Replies: 1
Views: 486
Hi Juulluu,
Just briefly before answering...
Hi Juulluu,
Just briefly before answering your question, have you trimmed off 7-8bp from the 5’ end of reads as is recommended for TruSeq libraries? If not I would recommend doing so, please see...
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Forum: Bioinformatics
05-26-2017, 05:15 AM
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Replies: 10
Views: 924
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Forum: Bioinformatics
05-26-2017, 04:42 AM
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Replies: 10
Views: 924
Excellent, sorry for being so ranty! :P
I...
Excellent, sorry for being so ranty! :P
I tried three different computers (PC/Mac) on site yesterday, tried posting from my phone (on Eduroam but on site as well) but then had to wait until I was...
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Forum: Bioinformatics
05-26-2017, 04:12 AM
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Replies: 10
Views: 924
I just replied this via email:
Hi David,
...
I just replied this via email:
Hi David,
Thanks for the sequences and the other update on SeqAnswers.
I had a look at your sequencing files, and came to the same conclusions. Both files...
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Forum: Bioinformatics
05-25-2017, 11:52 AM
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Replies: 10
Views: 924
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Forum: Bioinformatics
05-25-2017, 02:15 AM
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Replies: 10
Views: 924
There are a couple of things that could affect...
There are a couple of things that could affect the mapping efficiency, I'll list a few here:
- depending on the amplification strategy you might have to use --non_directional for mapping. This...
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Forum: General
05-22-2017, 02:45 PM
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Replies: 7
Views: 974
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Forum: General
05-22-2017, 05:20 AM
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Replies: 7
Views: 974
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Forum: Bioinformatics
05-12-2017, 12:33 PM
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Replies: 641
Views: 143,019
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Forum: Bioinformatics
05-12-2017, 07:32 AM
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Replies: 641
Views: 143,019
You should probably look at the coverage file...
You should probably look at the coverage file because this will also tell you how many counts you saw methylated or unmethylated. If you see 100% then I would suspect you saw only a single call for...
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Forum: Bioinformatics
05-11-2017, 01:51 PM
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Replies: 641
Views: 143,019
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Forum: Bioinformatics
04-24-2017, 07:36 AM
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Replies: 641
Views: 143,019
The score min function is linear (L), the first...
The score min function is linear (L), the first number is offset (which will be added to the final score which is determined by the number of mismatches, Ns, or insertions and deletions in the read),...
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Forum: Bioinformatics
04-18-2017, 01:04 AM
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Replies: 132
Views: 32,380
Very short reads generally don't tend to align...
Very short reads generally don't tend to align uniquely in bisulfite-seq mapping because the three letter alignment allows more ambiguous alignments. In that sense the shortness of reads sorts itself...
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