From 0b50312ab6a5c8d2eb1210c1505fe9979e7f13c6 Mon Sep 17 00:00:00 2001 From: Armin Toepfer Date: Mon, 18 Mar 2024 14:17:11 +0100 Subject: [PATCH] Aux files for Revio --- docs/faq/reports-aux-files.md | 73 +++++++++++++++++++++++++---------- 1 file changed, 53 insertions(+), 20 deletions(-) diff --git a/docs/faq/reports-aux-files.md b/docs/faq/reports-aux-files.md index 042a2c7..bb844f4 100644 --- a/docs/faq/reports-aux-files.md +++ b/docs/faq/reports-aux-files.md @@ -13,30 +13,63 @@ number of failed ZMWs. The following comments refer to the filters that are explained in the FAQ above. - ZMWs input : 1671 + ZMWs input : 1671 - ZMWs pass filters : 824 (49.31%) ┐ - ZMWs fail filters : 104 (6.22%) | Sum to 100% - ZMWs shortcut filters : 743 (44.46%) <- Low-pass ZMWs skipped by --all ┘ + ZMWs pass filters : 824 (49.31%) ┐ + ZMWs fail filters : 104 (6.22%) | Sum to 100% + ZMWs shortcut filters : 743 (44.46%) <- Low-pass ZMWs skipped by --all ┘ - ZMWs with tandem repeats : 10 (0.60%) <- With repeats larger than --min-tandem-repeat-length + ZMWs with tandem repeats : 10 (0.60%) <- With repeats larger than --min-tandem-repeat-length Exclusive failed counts - Below SNR threshold : 30 (28.85%) <- SNR below --min-snr. - Median length filter : 0 (0.00%) <- All subreads are <50% or >200% of the median subread length - Lacking full passes : 0 (0.00%) <- Fewer than --min-passes full-length (FL) reads - Heteroduplex insertions : 10 (9.62%) <- Single-strand artifacts - Coverage drops : 43 (41.35%) <- Coverage drops would lead to unreliable polishing results - Insufficient draft cov : 16 (15.38%) <- Not enough subreads aligned to draft end-to-end - Draft too different : 0 (0.00%) <- Fewer than --min-passes FL reads aligned to draft - Draft generation error : 3 (2.88%) <- Subreads don't agree to generate a draft sequence - Draft above --max-length : 0 (0.00%) <- Draft sequence is longer than --max-length - Draft below --min-length : 0 (0.00%) <- Draft sequence is shorter than --min-length - Reads failed polishing : 0 (0.00%) <- Too many subreads were dropped while polishing - Empty coverage windows : 2 (1.92%) <- At least one window has no coverage - CCS did not converge : 0 (0.00%) <- Draft has too many errors that can't be polished in time - CCS below minimum RQ : 0 (0.00%) <- Predicted accuracy is below --min-rq - Unknown error : 0 (0.00%) <- Rare implementation errors + Below SNR threshold : 30 (28.85%) <- SNR below --min-snr. + Median length filter : 0 (0.00%) <- All subreads are <50% or >200% of the median subread length + Lacking full passes : 0 (0.00%) <- Fewer than --min-passes full-length (FL) reads + Heteroduplex insertions : 10 (9.62%) <- Single-strand artifacts + Coverage drops : 43 (41.35%) <- Coverage drops would lead to unreliable polishing results + Insufficient draft cov : 16 (15.38%) <- Not enough subreads aligned to draft end-to-end + Draft too different : 0 (0.00%) <- Fewer than --min-passes FL reads aligned to draft + Draft generation error : 3 (2.88%) <- Subreads don't agree to generate a draft sequence + Draft above --max-length : 0 (0.00%) <- Draft sequence is longer than --max-length + Draft below --min-length : 0 (0.00%) <- Draft sequence is shorter than --min-length + Reads failed polishing : 0 (0.00%) <- Too many subreads were dropped while polishing + Empty coverage windows : 2 (1.92%) <- At least one window has no coverage + CCS did not converge : 0 (0.00%) <- Draft has too many errors that can't be polished in time + CCS adapter concatenation : 0 (0.000) <- Reads which are a concatenation of the adapter + CCS adapter palindrome : 0 (0.000) <- Miscalled adapters with reverse complemented inserts + CCS adapter residue : 0 (0.000) <- Reads that have one or more adapters close to either end + ZMW with full-length subread : 0 (0.000) <- fail_reads.bam reads that didn't generate consensus reads + ZMW with control failure : 0 (0.000) <- Reads that failed polishing and are spike-in controls + ZMW with control success : 0 (0.000) <- Reads that passed polishing and are spike-in controls + CCS below minimum RQ : 0 (0.00%) <- Predicted accuracy is below --min-rq + Unknown error : 0 (0.00%) <- Rare implementation errors + + Additional passing metrics + ZMWs missing adapters : 0 (0.000%) + + - - - - - - - - - - - - - - - : - - - - - + + HiFi Reads : 6 + HiFi Yield (bp) : 63,881 + HiFi Read Length (mean, bp) : 10,646 + HiFi Read Length (median, bp) : 10,289 + HiFi Read Length N50 (bp) : 10,439 + HiFi Read Quality (median) : 31 + HiFi Number of Passes (mean) : 9 + + =Q30 Reads : 5 + >=Q30 Yield (bp) : 54,336 + >=Q30 Read Length (mean, bp) : 10,867 + >=Q30 Read Length (median, bp): 10,439 + >=Q30 Read Quality (median) : 31 + + Base quality >=Q30 (bp) : 62,526 (97.9%) If run in `--by-strand` mode, please have a look at [the by-strand FAQ](/faq/mode-by-strand).\ If run in `--split-heteroduplexes` mode, please have a look at [the strand-aware FAQ](/faq/mode-heteroduplex-filtering).