t-neumann slamdunk issues

t-neumann / slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity

GNU Affero General Public License v3.0

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issues

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High background mutation of CtoT GtoA mutations

#164 Error-fre opened 1 week ago
1
summary - PCA done for group of samples not for samples, time points

#163 mmaslon opened 4 weeks ago
0
O

#162 tianwwwwww closed 2 months ago
0
alleyoop uttrates error

#161 mmaslon opened 2 months ago
11
slamdunk all: No tcount files and no error

#160 andtsouris opened 3 months ago
3
Application to Amplicon-Seq Libraries

#159 Rinyaveion opened 4 months ago
1
samplesheet

#158 mmaslon closed 5 months ago
4
/count folder empty

#157 Magisterh1 closed 5 months ago
1
Add cB file information to documentation

#156 isaacvock opened 6 months ago
0
Implement mixture model compatibility in full pipeline

#155 isaacvock opened 6 months ago
16
Implement mixture model compatibility

#154 isaacvock closed 6 months ago
5
Proposal for a new Alleyoop: convenient summary of `dump` output

#153 isaacvock opened 6 months ago
1
about 3utr numbers

#152 bioinformatica closed 6 months ago
4
Update stats.py

#151 BRYZAL closed 6 months ago
0
My slam-seq sequencing data only has 60-70% reads mapped to the genome

#150 bioinformatica closed 7 months ago
4
stranded library alignment

#149 ZiggeyQi closed 7 months ago
8
4SU labeled mRNA library built using the total RNAseq

#148 bioinformatica opened 7 months ago
7
about pair-end data

#147 bioinformatica closed 7 months ago
1
About calculating T>C reads CPM

#146 bioinformatica closed 7 months ago
10
IndexError: list index out of range errror when running alleyoop tcperreadpos

#145 BRYZAV closed 7 months ago
11
So many T2C conversion in no-4sU treated control samples

#144 realzhang closed 6 months ago
3
strand-specific SLAM-seq analysis

#143 ZiggeyQi closed 8 months ago
8
alleyoop dedup, samtools failed to create index because reads are not sorted

#142 algaebrown closed 9 months ago
2
Please help me to understand why we need alleyoop collapse.

#141 realzhang closed 7 months ago
3
mapping skipped sorting and indexing

#140 Error-fre closed 7 months ago
12
Please help me understand the output format of alleyoop dump.

#139 realzhang closed 9 months ago
4
mRNA half life calculation

#138 ZoeyYang912 closed 9 months ago
11
Errors with Slamdunk Count / Alleyoop Utrrates

#137 zaroogz closed 9 months ago
25
KeyError: "tag 'XI' not present". what does identity value mean?

#136 zhouyjjj opened 1 year ago
4
RuntimeError("Error while executing command: \"" + cmd + "\"")

#135 aishwarya-gondane closed 6 months ago
5
Samplesheet (see Sample file format ) or a list of all sample BAM/FASTA(gz)/FASTQ(gz) files (wildcard * accepted).

#134 Umair1441 opened 1 year ago
15
Try to run Slamdunk but failed

#133 Umair1441 closed 1 year ago
13
Regions with overlapping 3'UTRs annotated

#132 os306 closed 9 months ago
6
Issue installing slamdunk

#131 airiskic closed 1 year ago
1
UTR regions

#130 ChristianRohde closed 1 year ago
1
Trimmed reads caused slamdunk to stop at count

#129 tiffge closed 1 year ago
3
Effect of --slam-seq 2 parameter in NextGenMap call?

#128 isaacvock closed 1 year ago
2
How to interpret the bigwig values?

#127 gdolsten closed 9 months ago
3
DESeq2 for SLAM-seq

#126 gdolsten opened 1 year ago
7
map function fails part way through samples

#125 tiffge closed 1 year ago
18
Dockerfile bugged

#124 mattheatley opened 1 year ago
1
Downstream analysis

#123 paulinarosales closed 1 year ago
1
Genomic locations of the TC reads

#122 aishwarya-gondane closed 1 year ago
3
3'UTR length

#121 Choopanian-Peyman opened 1 year ago
4
Are alleyoop rates and multiqc plots snp corrected?

#120 seb-mueller closed 6 months ago
3
Correlation half-life calculation and DESeq2?

#119 quarkaffi closed 2 years ago
7
Use slamdunk -all get the filter dicrectory "_mapped_filtered.bam " file just 8kb?

#118 lillianj97 closed 6 months ago
31
slamdunk snp(varscan2) missing SNP around INDEL

#117 dyinboisry4u closed 6 months ago
9
RuntimeError while executing command slamdunk map

#116 cz0430 closed 6 months ago
2
Question about "-e" parameter

#115 bocheng97 closed 6 months ago
1