Data from: CHOPER filters enable rare mutation detection in complex mutagenesis populations by next-generation sequencing

Salehi F, Baronio R, Idrogo-Lam R, Vu H, Hall LV, Kaiser P, Lathrop R

Date Published: February 23, 2015

DOI: http://dx.doi.org/10.5061/dryad.mv827

 

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Title ACAGTG1_part1.fq
Description M237I_ACS sample/ forward reads/ part 1 (please join with ACAGTG1_part2.fq for a complete file). This sample corresponds to ACS mutagenesis performed on the p53 core domain containing the cancer mutant M237I. No selective pressure for p53 activity was applied. This sample controls for, and allows analysis of, the diversity of the ACS library.
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Title ACAGTG1_part2.fq
Description M237I_ACS sample/ forward reads/ part 2 (please join with ACAGTG1_part1.fq for a complete sample). This sample corresponds to ACS mutagenesis performed on the p53 core domain containing the cancer mutant M237I. No selective pressure for p53 activity was applied. This sample controls for, and allows analysis of, the diversity of the ACS library.
Download ACAGTG1_part2.fq.bz2 (453.4 Mb)
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Title ACAGTG2_part1.fq
Description M237I_ACS sample/ reverse reads/ part 1(please join with ACAGTG2_part2.fq for a complete sample). This sample corresponds to ACS mutagenesis performed on the p53 core domain containing the cancer mutant M237I. No selective pressure for p53 activity was applied. This sample controls for, and allows analysis of, the diversity of the ACS library.
Download ACAGTG2_part1.fq.bz2 (838.8 Mb)
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Title ACAGTG2_part2.fq
Description M237I_ACS sample/ reverse reads/ part 2 (please join with ACAGTG2_part1.fq for a complete sample). Corresponds to ACS mutagenesis performed on the p53 core domain containing the cancer mutant M237I. No selective pressure for p53 activity was applied. This sample controls for, and allows analysis of, the diversity of the ACS library.
Download ACAGTG2_part2.fq.bz2 (521.9 Mb)
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Title CAGATC1.fq
Description M237I_RESCUE sample/ forward reads. Identical to M237I_ACS sample except that transformants were selected for active p53 by culturing the cells in media lacking uracil, thus requiring active p53 for growth.
Download CAGATC1.fq.bz2 (872.5 Mb)
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Title CAGATC2.fq
Description M237I_RESCUE sample/ reverse reads. Identical to M237I_ACS sample except that transformants were selected for active p53 by culturing the cells in media lacking uracil, thus requiring active p53 for growth.
Download CAGATC2.fq.bz2 (922.2 Mb)
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Title TGACCA1_part1.fq
Description M237I sample/ forward reads/ part 1 (please join with TGACCA1_part2.fq for a complete sample). Represents the unprocessed p53 core domain that contains the cancer mutation M237I but no other introduced mutations. This sample was prepared to analyze and control the baseline error rates associated with the procedure, as well as the intrinsic NGS sequencing error rates.
Download TGACCA1_part1.fq.bz2 (838.8 Mb)
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Title TGACCA1_part2.fq
Description M237I sample/ forward reads/ part 2 (please join with TGACCA1_part1.fq for a complete sample). Represents the unprocessed p53 core domain that contains the cancer mutation M237I but no other introduced mutations. This sample was prepared to analyze and control the baseline error rates associated with the procedure, as well as the intrinsic NGS sequencing error rates.
Download TGACCA1_part2.fq.bz2 (268.3 Mb)
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Title TGACCA2_part1.fq
Description M237I sample/ reverse reads/ part 1 (please join with TGACCA2_part1.fq for a complete sample). Represents the unprocessed p53 core domain that contains the cancer mutation M237I but no other introduced mutations. This sample was prepared to analyze and control the baseline error rates associated with the procedure, as well as the intrinsic NGS sequencing error rates.
Download TGACCA2_part1.fq.bz2 (838.8 Mb)
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Title TGACCA2_part2.fq
Description M237I sample/ reverse reads/ part 2 (please join with TGACCA2_part1.fq for a complete sample). Represents the unprocessed p53 core domain that contains the cancer mutation M237I but no other introduced mutations. This sample was prepared to analyze and control the baseline error rates associated with the procedure, as well as the intrinsic NGS sequencing error rates.
Download TGACCA2_part2.fq.bz2 (322.1 Mb)
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Title m237i1
Description The m237i p53 cancer mutant gene core domain sequence.
Download m237i1.fa (845 bytes)
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Title choper
Description The CHOPER filtering implementation in python.
Download choper.py (11.65 Kb)
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Title codons
Description Counting codons after applying CHOPER filters for statistical analysis.
Download codons.py (3.514 Kb)
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Title PhredFilter
Description Phred filtering code. To run, use the following: "java -jar PhredFilter.jar <input.fq file> <output file> <threshold>" For example: java -jar PhredFilter.jar TGACCA1.fq TGACCA1_out.fq 30 The output file will be P30_TGACCA1_out.fq
Download PhredFilter.jar (174.7 Kb)
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When using this data, please cite the original publication:

Salehi F, Baronio R, Idrogo-Lam R, Vu H, Hall LV, Kaiser P, Lathrop R (2015) CHOPER filters enable rare mutation detection in complex mutagenesis populations by next-generation sequencing. PLoS ONE 10(2): e0116877. http://dx.doi.org/10.1371/journal.pone.0116877

Additionally, please cite the Dryad data package:

Salehi F, Baronio R, Idrogo-Lam R, Vu H, Hall LV, Kaiser P, Lathrop R (2015) Data from: CHOPER filters enable rare mutation detection in complex mutagenesis populations by next-generation sequencing. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.mv827
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