Commit 8c191c4a authored by Lucile Broseus's avatar Lucile Broseus

Update README.md

parent 010f702e
......@@ -25,8 +25,6 @@ git clone https://github.com/seqan/seqan.git
make
```
Instead, you may also directly download the executable, compiled for Linux64.
* Jellyfish2
Currently, TALC makes use of k-mer counts table as dumped by Jellyfish2.
......@@ -73,8 +71,8 @@ If your long reads are reverse complement of your short reads, please add the op
> --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
talc $LReads \ # File containg the long reads, in fasta or 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
......@@ -86,8 +84,8 @@ talc $LReads \ # File containg the long reads, in fasta of fastq forma
So as to integrate known splice junctions, you need create a dump file containing k-mers which flank splice junctions and specify
```
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
talc $LReads \ # File containg the long reads, in fasta or fastq format
--SRCounts $dump \ # k-mer counts from your short reads dataset, as generated by Jellyfish dump
--junctions $junc \ # k-mer counts of a subset of k-mers flanking known splice junctions, as generated by Jellyfish dump
-k $kmerSize \ # Size k of the k-mers, must match the dump file
-o $out \ # Prefix for the output
......
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