Hi, Thanks for your software. I ran SALSA but unfortunately I didn't have satisfying result.
I applied the Arima mapping pipeline and got this statistics before SALSA:
perl $STATS $REP_DIR/$REP_LABEL.bam > $REP_DIR/$REP_LABEL.bam.stats
cat $REP_DIR/$REP_LABEL.bam.stats
All 50585700
All intra 47453287
All intra 1kb 3798461
All intra 10kb 2498813
All intra 15kb 2338248
All intra 20kb 2223609
All inter 3132413
My opinion is that I don't have enough PE for All intra 20kb. I am not sure but what do you think about this library ? ( I have a very good contig assembly of 1.3G species, 750 contigs, busco: 98%)
What's the input N50 of the assembly? Also, you would want to look at ALL_INTER as those are the inter-contig links that will be used for scaffolding. I do agree that it might be an artifact of the bad library.
Hi, Thanks for your software. I ran SALSA but unfortunately I didn't have satisfying result.
I applied the Arima mapping pipeline and got this statistics before SALSA:
My opinion is that I don't have enough PE for
All intra 20kb
. I am not sure but what do you think about this library ? ( I have a very good contig assembly of 1.3G species, 750 contigs, busco: 98%)