Consensus parameters giving worse sequence

[githubgig]

Hello,

When I use pychopper and consensus parameters, the sequence seems worse in all six frames somehow (see below). I understand the cluster sequences can't be compared one-to-one, these are just examples. I find a similar worse sequence pattern in other sequences in the consensus file.

Changed Parameters:
Process cDNA reads using pychopper, turn off for direct RNA:
run_pychopper: true
Options passed to pychopper:
pychopper_opts: "-k PCS109 -r report.pdf -A aln_hits.bed -S statistics.tsv -u unclassified.fq -w rescued.fq"

Consensus period (-1 means no consensus):
consensus_period: 500
Minimum consensus sample size:
consensus_minimum: 50
Maximum consensus sample size:
consensus_maximum: 150

@cluster_0 origin=cons_0_41:1 length=749 size=17279
GGGGTCATACTAAGCTATTCGGCTAGTTTTAATAGTCAACTAACAAATATACGGGACACGGGTATACGGTTAATCATCCTTGGCTAAATCCCCGCTTACAATATCGAGCAAATGTGTAATACATACATATGCATAAAATTATATTTGGATTGTTTGGCGTGACTTTATTAATATATATTAAAATAGTATCACCATTTTGATAAAATTCGTGATTATTTCCGGTTGCTACTATCGTAATTCAAAATGTTTCGCAACCATGTCTAATGCATGTGTATAAAATATTTTGTATATAAAGCGGTATTCTTCTGCTGATGGGGATCAAACCAAATTCATCTGCAAAATGAACTTCTACTATATCCTTCAAGCTATTACCGTCGCTGTGCTCTTCGTAGCTGCAGCCCAGGGCGGTGGTGATGGAAACCCTCCTCCAGCCTAATTCCAGCAATGGGAAATTGTGTTTCAAATATTAATTTTTGACATACAAAATATTAAATACCATTGACAAAATGCAAAATAAATGAGCTCAACTTAACATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTCAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

With Default Settings, I get the below sequence.
Process cDNA reads using pychopper, turn off for direct RNA:
run_pychopper: false
Options passed to pychopper:
pychopper_opts: ""

Consensus period (-1 means no consensus):
consensus_period: -1
Minimum consensus sample size:
consensus_minimum: 50
Maximum consensus sample size:
consensus_maximum: -150

@cluster_0 origin=rep_6_989:1 length=999 size=17636
CCGTGACAAGAAAGTTGTCGGTGTCTTTGTGTTTCTGTTGGTGCTGATATTGCTGGGATCAAACCAAATTCATCTGCAAAATGAACTTCTACTATATCCTTCAAGCTATTACCGTCGCTGTGCTCTTCGTAGCTGCAGCCCAGGGCGGTGGTGATGGAAACCCTCCTCCAGCCTAATTCCAGCAATGGGAAATTGTGTTTCAAATATTAATTTTTGACATACAAAATATTAAATACCATTGACAAAATGCAAAATAAATGAGCTCAACTCAAAAAAAAAAAAAAAAAAAAAAAAGAAGATAGAGCGACAGGCAAGTCACAAAGACACCGACAACTTTCTTGTCGTTTCCAGTATGCTTCGTTCGTTTCAGTGGTGTTTATGATCCATCATCTACCGTGACAAGAGGATTGTCGGTGTCTTTGTGACTTGCCTGTCGCTCTATCTTCTCTTTTTTTAAAAAAACGCAAAAGCCACTTGAAATTTATTATTTCTAATGCATTTAGGGACTGATCTCCGTAGAGACATGATCATCTTCACCTTTGCAAGAGATAGTTATTTTTATTGGTGCTATCTCCGGATAGATAACCACATTGCACTCCTTTCACGCCCGTCATTTCGAAGAATTGCGTCATAGTAGATCCCGTCAAAAAATCAAAACTGCCAATACTAGTCACTTTGACAACAGTGTATTTGGGACCATCGCCAGCAGCCAGTTTGACCAAAGATGTTGTGAACAACTTCATAGCCTCTTCCCTCTTTGCGCCCTCTATTTCTTCCGGTATAATGTCACCGAAAGCCTTAACCGACATCATGACGATAACAGCCACCAACAAAACAATCGATATCCAAGGTGAACATTGTGAGGCAACTCTTCGCAGACGTTTGGGATAACACGATCACAAGGATTTAATAATTCTGAGTTTACCGCACACAGAATTACATATCCCCAGCAATATCAGCACCAACAGAAACACAAAGACACCGACAACTTTCTTGTCA

I'd also like to know, with default settings (consensus_period: -1), what exactly is being output to the cluster_cons.fq file if it is not the consensus of the clusters?

Thanks.