Commit 949eb051 authored by Lucile Broseus's avatar Lucile Broseus

Update README.md

parent d95ebb6c
......@@ -72,7 +72,7 @@ If your long reads are reverse complement of your short reads, please add the op
```
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
--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
......@@ -81,11 +81,14 @@ talc $LReads \ # File containg the long reads, in fasta or fastq forma
**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
So as to integrate known splice junctions, you need create a dump file containing k-mers which flank splice junctions and activate the option:
> --junctions
Such that:
```
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
--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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