Hi!
I found that although using a threshold=4 on RADmarkers module the output table includes ClusterTags below this number.
my input was:
RADmarkers -t 4 -m 2 -v > RADmarkers.output
and as example the head of such output is:
ClusterID ClusterTags SegPattern Tag SAMPLE1 SAMPLE2 SAMPLE3 SAMPLE4 SAMPLE5 SAMPLE6 SAMPLE7 SAMPLE8 SAMPLE9
1 1 -------11 ATCGGAATGGAGACACACACAGGAGCTTATCTGTCCGGACGGAGACAACAGGAAGTGAAGAGATCAGATGTCAGTGACTGCAGAACTCAGCAGGGCAGAGCAGGGAAAGCATGCAGCTGTCAGAATTGGC NA NA NA NA NA NA NA 32 9
2 1 -------11 ATCGGAACGACACGGGGGTACAAGGTACCCCCGTTCTCGTGATCGGTGGGGGTCTCGTCACTGAGACCCCCAACGATCAGCAAGTTAGGCCCTATCCTGTGGATAGGGCCTAACTTGCTAGTGGCTGCAG NA NA NA NA NA NA NA 25 28
3 1 -------11 ATCGGAGGGGATCAACTACAATGGGTGGGGGAGGACAGGGGGGCTTATGGTAGGGGGGATATGTTGGGAGTTTGTAAATTTTATTGTATGTAAGAAAAAAAACTTTCAATAAAAACTTTATTTGATTTAA NA NA NA NA NA NA NA 75 77
....
Nevertheless, I sorted out by filtering values >= 4 in the output by using awk.
I thank you for this amazing protocol!!
Cheers,
J.Martin
Hi!
I found that although using a threshold=4 on RADmarkers module the output table includes ClusterTags below this number.
my input was:
RADmarkers -t 4 -m 2 -v > RADmarkers.outputand as example the head of such output is:
ClusterID ClusterTags SegPattern Tag SAMPLE1 SAMPLE2 SAMPLE3 SAMPLE4 SAMPLE5 SAMPLE6 SAMPLE7 SAMPLE8 SAMPLE9
1 1 -------11 ATCGGAATGGAGACACACACAGGAGCTTATCTGTCCGGACGGAGACAACAGGAAGTGAAGAGATCAGATGTCAGTGACTGCAGAACTCAGCAGGGCAGAGCAGGGAAAGCATGCAGCTGTCAGAATTGGC NA NA NA NA NA NA NA 32 9
2 1 -------11 ATCGGAACGACACGGGGGTACAAGGTACCCCCGTTCTCGTGATCGGTGGGGGTCTCGTCACTGAGACCCCCAACGATCAGCAAGTTAGGCCCTATCCTGTGGATAGGGCCTAACTTGCTAGTGGCTGCAG NA NA NA NA NA NA NA 25 28
3 1 -------11 ATCGGAGGGGATCAACTACAATGGGTGGGGGAGGACAGGGGGGCTTATGGTAGGGGGGATATGTTGGGAGTTTGTAAATTTTATTGTATGTAAGAAAAAAAACTTTCAATAAAAACTTTATTTGATTTAA NA NA NA NA NA NA NA 75 77
....
Nevertheless, I sorted out by filtering values >= 4 in the output by using awk.
I thank you for this amazing protocol!!
Cheers,
J.Martin