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Answer: snippy error
Answer: TSS of protein coding genes
TSS of protein coding genes
Answer: vcf not indexing
Comment: Hybrid assembly Pacbio- Nanopore
Answer: vg call is time consuming
Answer: FDR and Bonferroni
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Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you for this advice , but when reading the documentation of split2 I found that it generates multiple files for the same fastq file. …
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
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ATpoint
81k
I will delete this as it - obviously - does not belong into this thread.
Comment: STAR aligner options
by
theophile
• 0
I searched the different options to increase the sensitivity. As per `--seedSearchStartLmax`, I found several answer from Alexander Dobin o…
Comment: STAR aligner options
by
theophile
• 0
Sorry, I was a bit confused by the layout, thanks for editing and clarifying!
Answer: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I want to calculate the mismatch rate on base-level, samtools stats in.bam | grep "error rate" | cut -f 2,3 error rate: 2.0…
Answer: Hybrid assembly Pacbio- Nanopore
by
colindaven
6.2k
If you have sufficient coverage of Pacbio HiFi reads - I think 30- 50X - then just use the Hifiasm https://github.com/chhylp123/hifiasm. It…
Answer: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
kayah
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you should run JoinLayers() before FindAllMarkers()!!
Answer: Error occurs when migrate-n software performs "make mpis"
by
lingxue
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Thank you very much. I will try to install it again according to your suggestion.
Comment: Only one read per run - Trying to use CellRangerv7
by
GenoMax
140k
https://www.ncbi.nlm.nih.gov/sra/?term=SRR16053948 Metadata indicates that this is: > Single-cell combinatorial-indexing RNA-sequencing (…
Comment: Paired layout, but one fastq file
by
GenoMax
140k
There is a BAM file available here: https://sra-pub-src-2.s3.amazonaws.com/SRR14667226/CTRL_possorted_genome_bam.bam.1 Please get that wit…
Comment: Only one read per run - Trying to use CellRangerv7
by
dsull
★ 5.6k
1. This is a comment, not an answer. Please don't post it as an answer. :) 2. This is sci-rna-seq, not 10x rna-seq. CellRanger would not …
Comment: Only one read per run - Trying to use CellRangerv7
by
Sky
▴ 10
Sorry for the delayed reply. I have included my code and the output from downloading the four files. Each dataset only resulted in one fast…
Answer: FDR and Bonferroni
by
joe
▴ 470
> Any idea why this is happening? For example, I got 1064 significant > probes from raw p-values, but only 18 from Bonferroni correction, a…
Comment: Paired layout, but one fastq file
by
Sky
▴ 10
I am also having a similar issue where there is only one fastq file but no bam file available so from my understanding I can't use bamtofas…
Comment: convert cds to seurat object
by
sooni
▴ 20
Yes, I tried with `as.Seurat`. But there is an error follwing: Error: `No data in provided assay - logcounts`. How can I solve this problem?
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