Comments (4)
Dear Rex Han,
If I understand you correctly, then I am afraid that AdapterRemoval cannot handle your data.
You write that your reads look like this [1]:
a. r1: barcode1-forwardprimer-sequence
r2: barcode2-reverseprimer-sequence
b. r1: barcode2-reverseprimer-sequence
r2: barcode1-forwardprimer-sequence
However, AdapterRemoval expects the following [2]:
a. r1: barcode1-sequence-forwardprimer
r2: barcode2-sequence-reverseprimer
b. r1: barcode2-sequence-reverseprimer
r2: barcode1-sequence-forwardprimer
That is to say that reads must start with a barcode, then the sequence, and finally end with an adapter. If your data does not look like that, then you cannot use AdapterRemoval and it is unlikely that support for the kind of layout you describe will be added.
However, if your data actually matches what AdapterRemoval requires [2], then you can perform the trimming and demultiplexing as follows:
Firstly, you will need to specify two sets of barcodes for each sample:
$ cat my_barcodes.txt
Sample1a barcode1 barcode2
Sample1b barcode2 barcode1
And secondly, you will need to specify two sets of adapters for use with --adapter-list:
$ cat my_adapters.txt
forwardprimer reverseprimer
reverseprimer forwardprimer
Once you have done that, then you can run with those lists AdapterRemoval as follows (adding your own input/output/trimming/etc options):
$ AdapterRemoval --adapter-list my_adapters.txt --barcode-list my_barcodes.txt ...
You will get two sets of output files per sample (e.g. Sample1a and Sample1b), but it's pretty simple to combine those afterwards. Note also that this will run slower than regular demultiplexing, since AdapterRemoval will try both sets of adapters for each read, regardless of the barcode.
Best,
Mikkel
from adapterremoval.
Dear Dr. Schubert,
thanks for your quick reply and I apologize for my confusing statement.
adapterremoval can only handle with one-orientation data as manpage said,
The first barcode is then compared to first N_1 bases of the mate 1 read, and the second barcode is compared to the first N_2 bases of the mate 2 read.
could you help add a function that automatically handle with mixed-orientation data,
(1) compare first barcode to r1, second barcode to r2, generate r1_1 and r2_1
(2) then first barcode to r2_unidentified, second barcode to r1_unidentified, generate r1_2 and r2_2
(3) finally cat r1_2 >> r1_1, cat r2_2 >> r2_1, and provide new data statistics
anyway, adapterremoval is an awesome software. my function request may ask too much.
thank you for putting my request into your consideration and feel free to make your own decision.
wish everything goes well with you. :)
from adapterremoval.
Dear Rex Han,
I'll think about adding functionality to AR to handle this.
But it seems like a very unusual situation, so I'm honestly not sure that it is worthwhile.
One possibility might be to allow multiple sets of barcodes per sample, which could perhaps also be useful in other situations, but from what I understand of your protocol you'd still need to provide both combinations of adapter sequences using --adapter-list
.
Best,
Mikkel
from adapterremoval.
Dear Dr. Schubert,
Glad to hear from you.
Thanks, I'll try this --adapter-list
.
wish everything goes well with u.
from adapterremoval.
Related Issues (20)
- --combined-output generates strange GC% distribution in fastqc reports HOT 4
- stdout and stderr reversed? HOT 1
- homebrew/science was deprecated HOT 1
- Adapter Removal running error HOT 2
- Internal barcodes HOT 5
- Support JSON log output HOT 3
- Add option for singular 'combined' output FASTQ files HOT 5
- Input file is overwritten and cut off HOT 3
- Adapters Not Being Trimmed (Apparently)? HOT 2
- collapse with SE reads HOT 3
- installation Adapterremoval with Conda HOT 2
- AdapterRemoval v3 Feedback HOT 12
- remove adapters sequences from BGI/MGI platform HOT 1
- combine with other QC tools HOT 1
- How to interpret the outputs of the multiple inputs after trimming? HOT 4
- New version of catch.hpp needed for glibc >= 2.34 HOT 1
- [feature request] Add support for GNU make's staged install via DESTDIR flag HOT 1
- support .gz format fastq as input HOT 1
- adapterremoval add windows version HOT 2
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 adapterremoval.