Commit ff5e8985 authored by Lucile Broseus's avatar Lucile Broseus

Update README.md

parent da78492c
......@@ -3,9 +3,24 @@
TALC is an hybrid Long Read correction method tailored for RNA-seq data.
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**Requirements:**
*
* Compilation
To compile from the source, you will need a **gcc version > 5** (for c++14).
TALC is built upon the SeqAn2 C++ library (https://github.com/seqan/seqan).
SeqAn2 C++ library is already included as a third party folder.
Compile with:
`cd TALC-version-1.0`
`make`
Instead, you may also directly download the executable, compiled for Linux64.
* Jellyfish2
......@@ -50,6 +65,15 @@ in TALC, short and long read sequences must be in the same direction (the weight
If your long reads are reverse complement of your short reads, please add the option:
> --reverse
```
talc $LReads \ # File containg the long reads, in fasta of fastq format
--SRCounts $dump \ # k-mer counts from your short reads dataset, as generated by Jellyfish dump
-k $kmerSize \ # Size k of the k-mers, must match the dump file
-o $out \ # Prefix for the output
-t $num_threads # Number of threads
--reverse # Reverse complement Long Read sequences before correction
```
*Using known splice junctions*
So as to integrate known splice junctions, you need create a dump file containing k-mers which flank splice junctions and specify
......@@ -65,7 +89,3 @@ talc $LReads \ # File containg the long reads, in fasta of fastq forma
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**Dependencies**
TALC is built upon the SeqAn2 C++ library.
https://github.com/seqan/seqan
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