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This repository has been archived by the owner on Jan 26, 2022. It is now read-only.
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
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
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.
The text was updated successfully, but these errors were encountered:
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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.
The text was updated successfully, but these errors were encountered: