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UMIextract giving ValueError: Read sequence: NNNNN is shorter than pattern: NNNNNNNN
umi rna-seq written 8 weeks ago by diwasri • 0 • updated 8 weeks ago by i.sudbery ♦ 10k
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1
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189
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1
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Transferring UMI from paired-end read 2 to header of read 1
umi next-gen deduplication umitoools written 10 weeks ago by robert.gnuegge • 0 • updated 10 weeks ago by i.sudbery ♦ 10k
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Cellranger output .bam file does Not contain barcodes ( CB and UB )
velocyto umi barcodes chromium10x cellranger written 11 weeks ago by Gabriel • 90
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Demultiplex Novaseq run with mixed samples containing either UDI alone or UMI-UDI
umi rna-seq demultiplexing written 4 months ago by diwasri • 0 • updated 4 months ago by GenoMax ♦ 95k
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183
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Error with ReviewConsensusVariants by fgbio
software error umi next-gen fgbio written 5 months ago by dyg2 • 0
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302
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splicing with UMI barcodes - paired end illumina sequencing
illumina umi umitools splicing star written 8 months ago by snishtala03 • 40
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2
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258
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from BAM to BED passing cell barcodes
bed umi bam scrna barcode written 9 months ago by BrunoGiotti • 110
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1
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818
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1
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Expression cutoff for UMI
umi gene expression written 9 months ago by JulianC • 10 • updated 9 months ago by i.sudbery ♦ 10k
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How to analyze DNA data with UMI
bioinformatics umi next-gen sequencing written 10 months ago by deniselavezzari • 0 • updated 10 months ago by GenoMax ♦ 95k
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327
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Long read UMI
umi onp pacbio fastp written 10 months ago by lager • 0
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574
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Downsampling UMI reads
umi next-gen rna-seq written 12 months ago by Bedirhan • 0 • updated 11 months ago by Kevin Blighe ♦ 69k
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1
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760
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UMI read consensus calling
umi next-gen unique molecular identifier nanopore written 11 months ago by SemiQuant • 70 • updated 11 months ago by i.sudbery ♦ 10k
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How to remove duplicate reads / create consensus reads based on umi tags in 2nd fastq file?
umi written 12 months ago by William • 4.7k
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3
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8 follow
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Bulk RNA-Seq pipeline suggestion incorporating UMIs
bulk umi rna-seq written 13 months ago by steveh • 30 • updated 13 months ago by swbarnes2 ♦ 9.4k
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534
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UMI on the fastq header
illumina umi fastq umi-tools rna-seq written 13 months ago by Ati • 30
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Forum: Help make UMI-tools even better - take our survey
umi survey forum umi-tools written 15 months ago by i.sudbery ♦ 10k
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1
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Consensus reads from UMIs
umi dna-seq deduplication written 17 months ago by graeme.thorn • 50 • updated 17 months ago by finswimmer ♦ 14k
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342
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Question about deduplication with UMI-tools
umi deduplication sequencing written 18 months ago by Chadi Saad • 80 • updated 18 months ago by i.sudbery ♦ 10k
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1
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313
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1
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how to align sequences with extra bases in 5'
umi alignment written 20 months ago by hsu • 20
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UMI with MACS
macs umi chip-seq written 21 months ago by Richard • 580 • updated 21 months ago by i.sudbery ♦ 10k
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889
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Formating RNA-seq with UMIs in unmapped BAM files to UMI-tools compatible FASTQ files
pre-processing umi rna-seq written 22 months ago by graeme.thorn • 50
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Tool: MAGERI: a software tool for calling rare variants and detecting circulating tumor DNA from UMI-tagged high-throughput sequencing data
rare variant umi resequencing ctdna tool written 3.7 years ago by mikhail.shugay ♦ 3.4k • updated 24 months ago by alons • 270
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How to deduplicate UMI with mapping shift ?
umi written 2.0 years ago by tatsuomano • 20 • updated 2.0 years ago by i.sudbery ♦ 10k
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10 follow
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De-duplicate UMI at FASTQ level
umi fastq written 2.3 years ago by jomo018 • 610 • updated 2.0 years ago by Rituriya • 40
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9 follow
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add UMI sequences to fastq read name
illumina umi fastq written 2.0 years ago by User6891 • 300 • updated 2.0 years ago by i.sudbery ♦ 10k
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miRNA with UMI - any papers showing this improves accuracy?
umi mirna written 2.6 years ago by Richard • 580 • updated 2.0 years ago by Rituriya • 40
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mirdeep2: UMI information lost when reads are collapsed
umi mirdeep2 mirna written 2.0 years ago by Rituriya • 40
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Is Kallisto able to deal with UMIs and paired-end RNASeq?
umi kallisto rna-seq written 2.1 years ago by antgomo • 30 • updated 2.1 years ago by GenoMax ♦ 95k
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760
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how to find the UMi position?
umi alignment written 2.2 years ago by DNAseq • 0 • updated 2.2 years ago by h.mon ♦ 32k
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Faster UMI extraction from scRNA-Seq data
scrna-seq umi umi_tools rna-seq written 2.4 years ago by paulranum11 • 70 • updated 2.4 years ago by benformatics • 2.0k
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