From 6305825c3b9a77ea1480674dbcbb1f330c0a9993 Mon Sep 17 00:00:00 2001 From: Jessica Mattick <19544292+jmattick@users.noreply.github.com> Date: Thu, 27 Jun 2024 07:30:37 -0700 Subject: [PATCH] Fix multiplexed isoseq example (#60) Co-authored-by: Jessica Mattick --- docs/clustering/examples.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/clustering/examples.md b/docs/clustering/examples.md index bae4caa..36a5166 100644 --- a/docs/clustering/examples.md +++ b/docs/clustering/examples.md @@ -10,7 +10,7 @@ nav_order: 4 ### Single sample This is a toy dataset consisting of ~80k segmented reads (S-reads) from a Kinnex full-length RNA library. The original HiFi reads have already been segmented using Skera, so we can directly go into primer removal using lima and such. - + # Download toy S-read dataset $ wget https://downloads.pacbcloud.com/public/dataset/IsoSeq_sandbox/human_80k_Sreads.segmented.bam @@ -44,13 +44,13 @@ nav_order: 4 flnc.report.csv $ isoseq cluster2 flnc.bam transcripts.bam - + $ ls transcripts* transcripts.bam transcripts.bam.pbi transcripts.cluster_report.csv - + ### Multiplexed samples This is a 12-plex regular Iso-Seq (non-Kinex) run on Sequel II system consisting of ~3 million HiFi reads. @@ -63,7 +63,7 @@ nav_order: 4 $ wget https://downloads.pacbcloud.com/public/dataset/Kinnex-full-length-RNA/REF-primers/IsoSeq_v2_primers_12.fasta # Demux and primer removal - $ lima --isoseq --peek-guess m64307e_230628_025302.hifi_reads.bam IsoSeq_v2_primers_12.fasta output.bam + $ lima --overwrite-biosample-names --isoseq --peek-guess m64307e_230628_025302.hifi_reads.bam IsoSeq_v2_primers_12.fasta output.bam # Combine inputs $ ls output.IsoSeqX*bam > all.fofn