whale_merge.py

[cag134392]

Dear bulkvis team,

I'm trying to use your program to have the corrected reads for over-splitting which seems to be a common feature in my data. I'm trying to use whale_merge.py to get the fastq file for downstream analysis the program seems to run well and identify reads and even concatenade them but at the end I the fastq input is completely empty. I even try to adjust the -d 50000 parameter to several more and less cutoff and still don't get any. This is the code I use:

`python3 whale_merge.py -s
Original read count: 2189756
Un-fused reads: 2162765
Reads joined: 26991
Fused reads: 13378
New read count: 2176143
Total bases: 8986185817

             MIN    MAX  MEAN   N50

Original: 4 96900 4103 4341
Un-fused reads: 4 96900 4123 4346
To be fused: 124 12405 2557 3488
Fused read: 466 19120 5159 5336
New: 4 96900 4129 4350
Top 10 original reads by length:
1: 96900
2: 90594
3: 51861
4: 51510
5: 51501
6: 41520
7: 30328
8: 29367
9: 28218
10: 25478
Top 10 fused reads by combined length:
1: 19120
2: 18797
3: 18126
4: 17997
5: 17600
6: 16815
7: 16651
8: 16238
9: 16106
10: 16082
Top 10 reads after correction:
1: 96900
2: 90594
3: 51861
4: 51510
5: 51501
6: 41520
7: 30328
8: 29367
9: 28218
10: 25478
2189756 reads to process.
!!!!!!! 0
2189756 to process, 0 fused, 0 unfused, 0 written.

Thank you very much!

[cag134392]

any feedback?

[mattloose]

Ah - sorry - this was missed - I'll raise it with @alexomics