Comments (6)
Hi @kokyriakidis,
TrimGalore! already trims low-quality bases I think. Have a look at the FastQC reports from after the trimming to check the read qualities (these FastQC results are not shown in the MultiQC report, you need to look in results/trim_galore/fastqc
.
from methylseq.
Trim Galore removes poor qualities from the 3' end of sequence, but does not do this from the 5' end (as it is never really needed). If you have some special kind of BS-seq data I'd be happy to look at your FastQC report (the HTML file), to see if I have any recommendations.
On a related note, a close colleague of mine has recently written a tool to analyse raw sequencing files and try to figure out which kind of bisulfite sequencing experiment had been performed. The tool (Charades) is still kind of in alpha mode, but you are very welcome to give it a try! https://github.com/ChristelKrueger/Charades
from methylseq.
Regarding your second question: I haven't looked at the ENCODE-DCC pipeline myself, but you could either
- align the data genome-wide and just look at your genes of interest, or
- get the sequence of the genes of interest (and maybe some surrounding sequence) and use that as a custom genome
The latter approach will be a a lot quicker, but it might not be as accurate for repetitive regions within your genes of interest, and you will have to adjust the positions if you want to bring it back in line with other genome coordinates.
from methylseq.
@FelixKrueger
Thank you very much! You can check the fastq in this link:
These are the initial files:
https://wetransfer.com/downloads/1b780edcfca5363f09e74202cca1ebd020190325114013/08a8a71624bbad7ecf6db365789c066520190325114013/affc1f
These are after TrimGalore with default settings:
https://wetransfer.com/downloads/a88486a3a7c15ac09042a291f60673b220190325114819/e96bc14c81defea887f22aa21369c0e820190325114819/c7af3f
from methylseq.
Whoah, that looks quite wild indeed. Judging by the sequence composition, it doesn't look like a standard sequencing protocol, it rather looks like amplicon sequencing to me. Any chance this is targetting the PTPN22 gene, and nothing else? I would probably proceed with a standard trim_galore --paired file1 file2
command, followed by a default directional alignment, and see what you get. Cheers, Felix
from methylseq.
It is targeting PTPN22
but also the lns-1
gene
from methylseq.
Related Issues (20)
- Support for NuGEN Ovation RRBS HOT 2
- samplesheet input is not detecting entire values in sample column HOT 6
- Create metro map HOT 1
- Add gemBS option
- CG CHG and CHH with --comprehensive flag using bismark workflow HOT 8
- --rrbs and --emseq parameter and argument usage
- typo in samplesheet in README.md?
- Latest template merge completely broke dev branch (on AWS + Fusion) HOT 4
- Specify additional "genomes" of spike-in controls for downstream calculation of bisulfite conversion efficiency HOT 1
- Schematic for the methylseq pipeline
- bwameth pipeline skipping all bwameth steps when --fasta, --fasta_index, and --bwa_meth_index are provided. HOT 2
- AS-XS tag missing
- Write tests for samplesheet sample merging/grouping
- Adding --maxVariantFrac and --minOppositeDepth to MethylDackel (Bwameth option)
- Bwameth vs bismark HOT 1
- Multiple issues in the pipeline HOT 1
- samplesheet handling: different path + same filename gives an error
- Pipeline requires 72GB of RAM, even to test. HOT 1
- Preseq error
- Massive disk usage
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from methylseq.