MyConnectome RNA-seq QA Overview

Quality assurance metrics were computed for each session of RNA-seq data using FastQC and Picard.

Print table of alignment metrics

(obtained using Picard::CollectAlignmentSummaryMetrics.jar - metric definitions at https://broadinstitute.github.io/picard/picard-metric-definitions.html#AlignmentSummaryMetrics)

Mean SD
TOTAL_READS 3.358365e+07 9.332021e+06
PF_READS 3.358365e+07 9.332021e+06
PCT_PF_READS 1.000000e+00 0.000000e+00
PF_NOISE_READS 8.958333e-01 1.171280e+00
PF_READS_ALIGNED 3.358365e+07 9.332021e+06
PCT_PF_READS_ALIGNED 1.000000e+00 0.000000e+00
PF_ALIGNED_BASES 3.391769e+09 9.424790e+08
PF_HQ_ALIGNED_READS 3.264652e+07 9.050898e+06
PF_HQ_ALIGNED_BASES 3.297123e+09 9.140865e+08
PF_HQ_ALIGNED_Q20_BASES 3.240662e+09 9.038253e+08
PF_HQ_MEDIAN_MISMATCHES 2.500000e-01 4.375950e-01
PF_MISMATCH_RATE 5.606800e-03 3.946800e-03
PF_HQ_ERROR_RATE 5.590200e-03 3.950300e-03
PF_INDEL_RATE 1.101000e-04 2.090000e-05
MEAN_READ_LENGTH 1.010000e+02 0.000000e+00
READS_ALIGNED_IN_PAIRS 2.980101e+07 8.703743e+06
PCT_READS_ALIGNED_IN_PAIRS 8.821913e-01 4.209160e-02
BAD_CYCLES 1.250000e-01 3.342187e-01
STRAND_BALANCE 5.820780e-01 1.606400e-02
PCT_CHIMERAS 3.258583e-01 4.504160e-02
PCT_ADAPTER 0.000000e+00 0.000000e+00

Print table of rnaseq metrics

(obtained using Picard::CollectRnaSeqMetrics.jar - metric definitions at https://broadinstitute.github.io/picard/picard-metric-definitions.html#RnaSeqMetrics)

Mean SD
PF_BASES 6.646251e+09 1.811126e+09
PF_ALIGNED_BASES 6.645865e+09 1.811020e+09
RIBOSOMAL_BASES 0.000000e+00 0.000000e+00
CODING_BASES 2.202528e+09 7.315647e+08
UTR_BASES 1.522187e+09 4.624208e+08
INTRONIC_BASES 1.112084e+09 3.928677e+08
INTERGENIC_BASES 1.809065e+09 4.869813e+08
IGNORED_READS 0.000000e+00 0.000000e+00
PCT_RIBOSOMAL_BASES 0.000000e+00 0.000000e+00
PCT_CODING_BASES 3.268602e-01 4.059680e-02
PCT_UTR_BASES 2.277746e-01 2.277710e-02
PCT_INTRONIC_BASES 1.713799e-01 5.213090e-02
PCT_INTERGENIC_BASES 2.739853e-01 3.680680e-02
PCT_MRNA_BASES 5.546348e-01 5.950290e-02
PCT_USABLE_BASES 5.546027e-01 5.949990e-02
MEDIAN_CV_COVERAGE 7.831457e-01 6.257640e-02
MEDIAN_5PRIME_BIAS 2.309370e-02 6.401300e-03
MEDIAN_3PRIME_BIAS 2.967212e-01 4.332000e-02
MEDIAN_5PRIME_TO_3PRIME_BIAS 9.149010e-02 2.696420e-02

Plot RNA integrity number (RIN) across sessions

plot of chunk plotrin

Plot QA metrics across read positions

plot of chunk plotreadpos

Plot timeseries for QA variables across sessions with marginal histograms

plot of chunk plotts