t-neumann/slamdunk issues and pull requests

#162 - O

Issue - State: closed - Opened by tianwwwwww 2 months ago

#161 - alleyoop uttrates error

Issue - State: open - Opened by mmaslon 3 months ago - 11 comments

#160 - slamdunk all: No tcount files and no error

Issue - State: open - Opened by andtsouris 3 months ago - 3 comments

#159 - Application to Amplicon-Seq Libraries

Issue - State: open - Opened by Rinyaveion 4 months ago - 1 comment

#158 - samplesheet

Issue - State: closed - Opened by mmaslon 5 months ago - 4 comments

#157 - /count folder empty

Issue - State: closed - Opened by Magisterh1 6 months ago - 1 comment

#156 - Add cB file information to documentation

Pull Request - State: open - Opened by isaacvock 6 months ago

#155 - Implement mixture model compatibility in full pipeline

Pull Request - State: open - Opened by isaacvock 7 months ago - 16 comments

#154 - Implement mixture model compatibility

Pull Request - State: closed - Opened by isaacvock 7 months ago - 5 comments

#153 - Proposal for a new Alleyoop: convenient summary of `dump` output

Issue - State: open - Opened by isaacvock 7 months ago - 1 comment

#152 - about 3utr numbers

Issue - State: closed - Opened by bioinformatica 7 months ago - 4 comments

#151 - Update stats.py

Pull Request - State: closed - Opened by BRYZAL 7 months ago

#150 - My slam-seq sequencing data only has 60-70% reads mapped to the genome

Issue - State: closed - Opened by bioinformatica 7 months ago - 4 comments

#149 - stranded library alignment

Issue - State: closed - Opened by ZiggeyQi 7 months ago - 8 comments

#148 - 4SU labeled mRNA library built using the total RNAseq

Issue - State: open - Opened by bioinformatica 7 months ago - 7 comments

#147 - about pair-end data

Issue - State: closed - Opened by bioinformatica 7 months ago - 1 comment

#146 - About calculating T>C reads CPM

Issue - State: closed - Opened by bioinformatica 8 months ago - 10 comments

#145 - IndexError: list index out of range errror when running alleyoop tcperreadpos

Issue - State: closed - Opened by BRYZAV 8 months ago - 9 comments

#144 - So many T2C conversion in no-4sU treated control samples

Issue - State: closed - Opened by realzhang 9 months ago - 3 comments

#143 - strand-specific SLAM-seq analysis

Issue - State: closed - Opened by ZiggeyQi 9 months ago - 8 comments

#142 - alleyoop dedup, samtools failed to create index because reads are not sorted

Issue - State: closed - Opened by algaebrown 10 months ago - 2 comments

#141 - Please help me to understand why we need alleyoop collapse.

Issue - State: closed - Opened by realzhang 10 months ago - 3 comments

#140 - mapping skipped sorting and indexing

Issue - State: closed - Opened by Error-fre 10 months ago - 12 comments

#139 - Please help me understand the output format of alleyoop dump.

Issue - State: closed - Opened by realzhang 10 months ago - 4 comments

#138 - mRNA half life calculation

Issue - State: closed - Opened by ZoeyYang912 12 months ago - 11 comments

#137 - Errors with Slamdunk Count / Alleyoop Utrrates

Issue - State: closed - Opened by zaroogz about 1 year ago - 25 comments

#136 - KeyError: "tag 'XI' not present". what does identity value mean?

Issue - State: open - Opened by zhouyjjj about 1 year ago - 4 comments

#135 - RuntimeError("Error while executing command: \"" + cmd + "\"")

Issue - State: closed - Opened by aishwarya-gondane about 1 year ago - 5 comments

#134 - Samplesheet (see Sample file format ) or a list of all sample BAM/FASTA(gz)/FASTQ(gz) files (wildcard * accepted).

Issue - State: open - Opened by Umair1441 over 1 year ago - 15 comments

#133 - Try to run Slamdunk but failed

Issue - State: closed - Opened by Umair1441 over 1 year ago - 13 comments

#132 - Regions with overlapping 3'UTRs annotated

Issue - State: closed - Opened by os306 over 1 year ago - 6 comments

#131 - Issue installing slamdunk

Issue - State: closed - Opened by airiskic over 1 year ago - 1 comment

#130 - UTR regions

Issue - State: closed - Opened by ChristianRohde over 1 year ago - 1 comment

#129 - Trimmed reads caused slamdunk to stop at count

Issue - State: closed - Opened by tiffge over 1 year ago - 3 comments

#128 - Effect of --slam-seq 2 parameter in NextGenMap call?

Issue - State: closed - Opened by isaacvock over 1 year ago - 2 comments

#127 - How to interpret the bigwig values?

Issue - State: closed - Opened by gdolsten over 1 year ago - 3 comments

#126 - DESeq2 for SLAM-seq

Issue - State: open - Opened by gdolsten over 1 year ago - 7 comments

#125 - map function fails part way through samples

Issue - State: closed - Opened by tiffge over 1 year ago - 18 comments

#124 - Dockerfile bugged

Issue - State: open - Opened by mattheatley almost 2 years ago - 1 comment

#123 - Downstream analysis

Issue - State: closed - Opened by paurosales almost 2 years ago - 1 comment

#122 - Genomic locations of the TC reads

Issue - State: closed - Opened by aishwarya-gondane almost 2 years ago - 3 comments

#121 - 3'UTR length

Issue - State: open - Opened by Choopanian-Peyman almost 2 years ago - 4 comments

#120 - Are alleyoop rates and multiqc plots snp corrected?

Issue - State: closed - Opened by seb-mueller almost 2 years ago - 3 comments

#119 - Correlation half-life calculation and DESeq2?

Issue - State: closed - Opened by quarkaffi about 2 years ago - 7 comments

#118 - Use slamdunk -all get the filter dicrectory "_mapped_filtered.bam " file just 8kb?

Issue - State: closed - Opened by lillianj97 about 2 years ago - 31 comments

#117 - slamdunk snp(varscan2) missing SNP around INDEL

Issue - State: closed - Opened by dyinboisry4u about 2 years ago - 9 comments

#116 - RuntimeError while executing command slamdunk map

Issue - State: closed - Opened by cz0430 about 2 years ago - 2 comments

#115 - Question about "-e" parameter

Issue - State: closed - Opened by bocheng97 over 2 years ago - 1 comment

#114 - "More columns than column names" error message when running alleyoop utrrates

Issue - State: closed - Opened by cz0430 over 2 years ago - 7 comments

#113 - ReadCount to get number of reads mapped?

Issue - State: closed - Opened by my-linh-luu over 2 years ago - 2 comments

#112 - error in alleyoop summary

Issue - State: closed - Opened by beckedorff over 2 years ago - 12 comments

#111 - alleyoop utrrates output file extension

Issue - State: open - Opened by jvanbelzen almost 3 years ago

#110 - Index Files (*.bam.bai) Missing?

Issue - State: closed - Opened by jvanbelzen almost 3 years ago - 1 comment

#109 - Using DUNK for detection of RNA editing

Issue - State: closed - Opened by andreagillespie almost 3 years ago - 6 comments

#108 - SNP calling based on all samples vs no4SU samples

Issue - State: closed - Opened by crueckle almost 3 years ago - 12 comments

#107 - Signal at alternate contigs lost

Issue - State: closed - Opened by monikaperez almost 3 years ago - 1 comment

#106 - Multimapping influences output at read length of 152bp

Issue - State: closed - Opened by monikaperez almost 3 years ago - 1 comment

#105 - Multimapping is not default and bed file isn't used

Issue - State: closed - Opened by monikaperez almost 3 years ago - 1 comment

#104 - Extra tags + HISAT3 +

Issue - State: closed - Opened by aleighbrown about 3 years ago - 6 comments

#103 - error when running count dunk

Issue - State: closed - Opened by jonwruffin about 3 years ago - 3 comments

#102 - Help with Parameters (-fb, -c) for running SLAMDUNK; comparison of published data

Issue - State: closed - Opened by crueckle about 3 years ago - 19 comments

#101 - Slamdunk parallel processing

Issue - State: closed - Opened by bernt-matthias about 3 years ago - 1 comment

#100 - Filtering reads for having ≥2 T>C conversions

Issue - State: closed - Opened by os306 over 3 years ago - 15 comments

#99 - analysing HISAT-3N bam files

Issue - State: closed - Opened by pillailab over 3 years ago - 7 comments

#98 - missing DS tag

Issue - State: closed - Opened by bobermayer over 3 years ago - 2 comments

#97 - Calculating conversion rates other than T>C

Issue - State: closed - Opened by goeringr over 3 years ago - 5 comments

#96 - Slamdunk all command not working

Issue - State: closed - Opened by aishwarya-gondane over 3 years ago - 24 comments

#95 - Output .bam of T-C containing reads?

Issue - State: closed - Opened by snaqvi1990 over 3 years ago - 1 comment

#94 - default 12bp trimming from 5' end

Issue - State: closed - Opened by snaqvi1990 over 3 years ago - 3 comments

#93 - Alleyoop dedup

Issue - State: closed - Opened by snaqvi1990 over 3 years ago - 1 comment

#92 - slamdunk installation fails: Library not loaded: @rpath/libhts.2.dylib

Issue - State: closed - Opened by drowsygoat almost 4 years ago - 9 comments

#91 - can SLAM-DUNK be used on 10x based scSLAM-seq?

Issue - State: closed - Opened by jon-xu almost 4 years ago

#90 - 3' UTR file generation

Issue - State: closed - Opened by zsun89 almost 4 years ago - 3 comments

#89 - slamDunk for totalRNA kit

Issue - State: closed - Opened by kopardev almost 4 years ago - 2 comments

#88 - SlamDunk for smallRNA data

Issue - State: closed - Opened by jaqx008 almost 4 years ago - 26 comments

#87 - 3'UTR bed file

Issue - State: closed - Opened by peneder almost 4 years ago - 2 comments

#86 - Slamdunk Count: Paired-end slam-seq mapping with ngm

Issue - State: closed - Opened by penguinmeow about 4 years ago - 5 comments

#85 - [E::idx_find_and_load] errors

Issue - State: closed - Opened by shokohirosue about 4 years ago - 9 comments

#84 - Pathing issues

Issue - State: closed - Opened by Furciferi about 4 years ago - 5 comments

#83 - Multimapper-Reassignment Stragety

Issue - State: closed - Opened by iris-summer about 4 years ago - 3 comments

#82 - How to obtain half-life table?

Issue - State: closed - Opened by osamnsmr about 4 years ago - 8 comments

#80 - error in SNP dunk

Issue - State: closed - Opened by CharlotteAnne about 4 years ago - 4 comments

#79 - Update globalRatePlotter.R

Pull Request - State: closed - Opened by Hypertyz about 4 years ago

#78 - Alleyoop is not working properly

Issue - State: closed - Opened by Hypertyz over 4 years ago - 4 comments

#77 - Is slamdunk suitable for single cell SLAM-seq analysis

Issue - State: closed - Opened by pigraul over 4 years ago - 1 comment

#76 - error in alleyoop utrrates

Issue - State: closed - Opened by minaka1484 over 4 years ago - 17 comments

#75 - Permission denied trying to run globalRatePlotter.R

Issue - State: closed - Opened by FitzsimmonsCM over 4 years ago - 8 comments

#74 - Background TC counts

Issue - State: closed - Opened by BrianLohman over 4 years ago - 5 comments

#73 - minor update of code snippet to python3 required

Issue - State: closed - Opened by bsennblad over 4 years ago

#72 - Replace alignment step

Issue - State: closed - Opened by sarahet over 4 years ago - 2 comments

#71 - alleyoop utrrates does not estimate read length

Issue - State: closed - Opened by aparajitadutta over 4 years ago - 1 comment

#70 - Differential Expression for SLAM-seq

Issue - State: closed - Opened by aksenovavy over 4 years ago - 14 comments

#69 - slamdunk all Unable to locate files

Issue - State: closed - Opened by aparajitadutta over 4 years ago - 10 comments

#68 - error in alleyoop merge

Issue - State: closed - Opened by BrianLohman almost 5 years ago - 3 comments

#67 - High conversion rates in smallRNA control samples

Issue - State: closed - Opened by Enidanellani almost 5 years ago - 2 comments

GitHub / t-neumann/slamdunk issues and pull requests