epi2me-labs wf-transcriptomes issues

epi2me-labs / wf-transcriptomes

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What to do with the generated data

#97 CamillePhilippeSCI opened 5 days ago
0
Getting "Process `pipeline:assemble_transcripts (3)` terminated with an error exit status (1)" while trying to get transcript count table from cDNA-Seqq

#96 AlvaroBernardino closed 4 days ago
1
de_analysis.R: Creating counts dataframe changes counts variable from matrix to 'named' integer

#95 damioresegun opened 1 week ago
4
More than 2 conditions in the sample sheet

#94 CWYuan08 opened 2 weeks ago
4
ERROR ~ Error executing process > 'pipeline:preprocess_ref_annotation

#93 Rpowellnz closed 1 week ago
3
ERROR ~ Error executing process > 'pipeline:preprocess_reads (8)'

#92 CWYuan08 opened 3 weeks ago
3
main.nf error

#91 shelgueta opened 1 month ago
3
Incompatability with nextflow version 24.04.01?

#90 Brynjar-H opened 1 month ago
2
improve annotations

#89 sqwwww closed 2 weeks ago
2
Error in deAnalysis when doing 'reference guided' analysis

#88 KatrinMoller opened 2 months ago
6
Halt at preprocess reads when using custom primers in pychopper

#87 claumer closed 3 weeks ago
3
Output DGE analysis files omit gene names

#86 sydjo07 opened 2 months ago
5
Missing transcriptome level differential expression analysis in the latest version

#85 alyazeeditalal opened 2 months ago
3
How to manipulate wf-transcriptomes with docker, and what is the exact command?

#84 haozhang501 opened 2 months ago
1
Kit used for cDNA synthesis

#83 AlvaroBernardino opened 2 months ago
5
Error executing process > 'pipeline:differential_expression:build_minimap_index_transcriptome'

#82 kamegh opened 2 months ago
14
Error in executing process pipeline:differential_expression:map_transcriptome

#81 alyazeeditalal opened 3 months ago
4
How to run with annotation files （gff） from EVM merging

#80 aaannaw closed 3 weeks ago
3
fastcat: unrecognized option '--histograms' and csvtk: command not found

#79 hgingras opened 3 months ago
7
Invalid sample sheet: values in 'barcode' column are incorrect format.

#78 GianlucaMattei closed 2 months ago
2
Error about minimap2

#77 Musketeer-D closed 2 weeks ago
4
Issue with GTF (values in 'transcripts$tx_strand' must be "+" or "-")

#76 physnano opened 3 months ago
8
Crash on searching fastq files

#75 GianlucaMattei closed 1 month ago
2
Singularity docker image problem

#74 KatrinMoller closed 3 months ago
0
The mapping step statistics

#73 CHENAO-QIAN closed 1 month ago
3
Integrating short- and long-read RNAseq

#72 YIGUIz closed 2 months ago
1
More than two conditions

#71 CHENAO-QIAN closed 3 months ago
2
Singularity Python issue

#70 mdhitch closed 1 month ago
5
bpipe error

#69 kristianunger closed 3 months ago
2
Why are my BAM files so small?

#68 phillip-richmond-alamya opened 4 months ago
5
Error in Differential expression analysis

#67 KatrinMoller closed 3 months ago
10
Options to add transcript ensembl id to the aln bam file

#66 Yijun-Tian closed 4 months ago
2
Running multiple files in parallel

#65 BethHudson-Lund opened 4 months ago
4
Buil_minimap_index_transcriptome error

#64 mdhitch closed 3 months ago
6
Why did you remove the `--transcriptome_source` denovo option ?

#63 pbuendia closed 1 month ago
7
update readme

#62 satriobio closed 4 months ago
2
Fix samplesheet requirements

#61 phillip-richmond-alamya closed 5 months ago
2
Docker in Docker workflow execution

#60 remyvander closed 4 months ago
3
Dockerfile

#59 agata-sm closed 5 months ago
2
How to install EPI2ME in the cluster?

#58 WQQIGDB closed 3 months ago
4
Clarify/correct filtering for edgeR D.E. analysis?

#57 lweasel opened 5 months ago
5
makeReport runs out of memory

#56 jdiazsupsi closed 3 months ago
8
Minimap2 running on a single core

#55 KatrinMoller closed 4 months ago
6
How to set the 'min_feature_expr' parameter to preserve rare transcripts?

#54 WQQIGDB closed 3 months ago
2
Which references to use to assure compatibility with JAFFAL

#53 mdhitch closed 1 month ago
7
Attempting to run workflow with demo data fails

#52 emsisson closed 5 months ago
8
[ERRO] open bam_bundles/000000000_chr1:14359:6208325_bundle.bam: invalid argument

#51 santiago-es closed 1 month ago
7
Understanding origin and significance of gene, transcript, and isoform MSTRG results

#50 cea295933 closed 4 months ago
8
Prokaryotes and multi-mapping reads

#49 kneubehl closed 6 months ago
1
Fix for JAFFA in WSL

#48 cjops closed 3 months ago
3