SIIIRTMg_call2: JACUSA2 output for call-22 on SIIIRTMg condition in Zhou et....
In dieterich-lab/JACUSA2helper: Post-processing for JACUSA2 output
SIIIRTMg_call2 R Documentation
JACUSA2 output for call-22 on SIIIRTMg condition in Zhou et. al 2018 data
Description
Zhou2018 et al. 2018 map RNA modification of pseudouridine Ψ by chemically modifying
pseudouridines with carbodiimide (+CMC) and detecting arrest events that are induced by reverse
transcription stops in high-throughput sequencing under 3 different conditions (HIVRT, SIIIMn, and
SIIIMg).
Result are for running JACUSA2 call-2 on processed pairwise +CMC and -CMC(control) data in SIIIRTMg condition are presented.
Usage
data(SIIIRTMg_call2)
Format
a tibble with 18 elements:
id: Character string representing a unique identifier - created from contig, start, [end], and strand.
contig: Character string representing the contig of the variant
start: Numeric position of variant (>=0)
end: Numeric corresponds to "start + 1"
name: Character string. Name of used method call-2
score: Numeric value representing the test-statistc. Higher values indicate more divergent pileups
strand: Character representing strand information; "+", "-", or "."(no strand information available)
bases: Numeric tibble with representing counts for A, C, G, and T base calls.
cov: Numeric value indicating the read coverage for this site
backtrack1: Character - indicator if backtracking was used for condition 1.
backtrack2: Character - indicator if backtracking was used for condition 2.
backtrackP: Character - indicator if backtracking was used for condition pooled condition.
reset1: Character - indicator if default estimation was unstable with for condition 1.
reset2: Character - indicator if default estimation was unstable with for condition 2.
resetP: Character - indicator if default estimation was unstable with for pooled condition.
info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
Details
Check Section "Reverse transcriptase arrest events"
https://github.com/dieterich-lab/JACUSA2/blob/master/manual/manual.pdf
for details on pre-processing and mapping primary sequencing data.
References
Zhou, K. I.; Clark, W. C.; Pan, D. W.; Eckwahl, M. J.; Dai, Q. & Pan, T.
Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing
RNA Biology, Informa UK Limited, 2018 , 15 , 892-900
dieterich-lab/JACUSA2helper documentation built on March 1, 2023, 12:09 a.m.
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| SIIIRTMg_call2 | R Documentation |
JACUSA2 output for call-22 on SIIIRTMg condition in Zhou et. al 2018 data
Description
Zhou2018 et al. 2018 map RNA modification of pseudouridine Ψ by chemically modifying pseudouridines with carbodiimide (+CMC) and detecting arrest events that are induced by reverse transcription stops in high-throughput sequencing under 3 different conditions (HIVRT, SIIIMn, and SIIIMg). Result are for running JACUSA2 call-2 on processed pairwise +CMC and -CMC(control) data in SIIIRTMg condition are presented.
Usage
data(SIIIRTMg_call2)
Format
a tibble with 18 elements:
id: Character string representing a unique identifier - created from contig, start, [end], and strand.
contig: Character string representing the contig of the variant
start: Numeric position of variant (>=0)
end: Numeric corresponds to "start + 1"
name: Character string. Name of used method call-2
score: Numeric value representing the test-statistc. Higher values indicate more divergent pileups
strand: Character representing strand information; "+", "-", or "."(no strand information available)
bases: Numeric tibble with representing counts for A, C, G, and T base calls.
cov: Numeric value indicating the read coverage for this site
backtrack1: Character - indicator if backtracking was used for condition 1.
backtrack2: Character - indicator if backtracking was used for condition 2.
backtrackP: Character - indicator if backtracking was used for condition pooled condition.
reset1: Character - indicator if default estimation was unstable with for condition 1.
reset2: Character - indicator if default estimation was unstable with for condition 2.
resetP: Character - indicator if default estimation was unstable with for pooled condition.
info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".
Details
Check Section "Reverse transcriptase arrest events" https://github.com/dieterich-lab/JACUSA2/blob/master/manual/manual.pdf for details on pre-processing and mapping primary sequencing data.
References
Zhou, K. I.; Clark, W. C.; Pan, D. W.; Eckwahl, M. J.; Dai, Q. & Pan, T. Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing RNA Biology, Informa UK Limited, 2018 , 15 , 892-900
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