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Recent Replies
Comment: Y-axis break in Volcano Plot
by
GenoMax
151k
> Any help is appreciated
You should consider upvoting and validating (accepting, green check mark) comments/answers you have received on …
Comment: Isoform analysis after quantification with Salmon/Star
by
rajdeepboral00
▴
70
Thank you for your detailed reply
Answer: Nanopore data analysis
by
colindaven
7.6k
- Merge bams - yes. (why do you have so many ?). Merging fastqs before creating bams is easier (cat *.fastq.gz ) than bam merging.
- 150…
Answer: What is the difference between norm --multiallelics -any versus --atomize?
by
ashotmarg2004
▴
130
There is a related discussion here: https://github.com/samtools/bcftools/issues/2142
Answer: checking the sequences that share origin
by
GenoMax
151k
Without the presence of [**UMI**][1] in data, it would be difficult to say with certainty that a pair of sequences share an identical origi…
Comment: Bambu on illumina short reads sequencing
by
Rob
7.1k
I'll agree with GenoMax here. While the approach of bambu shares several methodological underpinnings with methods used for short-read qua…
Comment: Nanopore data analysis
by
GenoMax
151k
Data volume is going to depend on the amount of sequencing. Was this a PromethION flowcell? Tool should handle the data as long as you have…
Comment: Bambu on illumina short reads sequencing
by
GenoMax
151k
Did you see a recent thread --> https://www.biostars.org/p/9612865/ which delineates standard methods for short-read data.
Bambu is meant…
Comment: Nanopore data analysis
by
sarahmanderni
▴
130
The overall size for all bam files is around 150 GB. Is this common for nanopore and does this tools handle this volume of data?
Thanks fo…
Comment: Nanopore data analysis
by
GenoMax
151k
How about using `modkit` provided by Nanopore for methylation data analysis: https://github.com/nanoporetech/modkit
Comment: Significant reads loss after fastp
by
GenoMax
151k
Will refer you back to my comment above. Don't be fixated on the Q scores. You don't say what kind of data this is but it may still align f…
Comment: Better splitting of mutliallelic sites then bcftools norm --m-any
by
gernophil
▴
130
Because this question just received an upvote: I used `vt decompose -s` back in the days, but I think bcftools now also makes you choose th…
Comment: Significant reads loss after fastp
by
SpliceAndScript
•
0
I have attached the phred score image of my reads, your opinion will be appreciated.
Comment: Significant reads loss after fastp
by
SpliceAndScript
•
0
I have RNA-seq data and here I am attaching the fastqc report image of ![enter image description here][1]my reads before and after running …
Comment: Data of microarray
by
Peter
•
0
sorry but I do not have input file. If you have can you offer to me?
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