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Answer: Problem with Mirdeep2 and Randfold output
Comment: Trying to write bwa mem -> samtools view -> samtools sort loop
C: Extract fasta sequences from a file using a list in another file.
A: Extract fasta sequences from a file using a list in another file.
How to comparing two bacterial genomes and find the mutation, rearrangement etc.
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
Answer: Korean reference file
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Recent Replies
Answer: Problem with Mirdeep2 and Randfold output
by
otieno43
▴ 30
I sorted this out by first removing white space in the first line of the reference genome. Then indexed, the ran the mapper.pl script follo…
Comment: Questions about a bug when transferring cram file to bam file
by
GenoMax
141k
Just to be certain, you are saying that if OP runs `samtools view` without the explicit reference it will be automatically downloaded from …
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa). I'm assuming your hg38.fa is not the sa…
Comment: What happened to Tombo Re-squiggle
by
Ram
43k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: What happened to Tombo Re-squiggle
by
Joseph
• 0
Hi, Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate com…
Answer: change gene IDs to gene name in RNAseq
by
Trivas
★ 1.7k
This has been answered a million times on this forum, see here https://www.biostars.org/p/430015/
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome
by
colindaven
6.3k
It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**. `Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Elisabeth Gasteiger
★ 2.4k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates
by
valentinatsar
• 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
Ok I made this into an answer. Could you please accept it as such.
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How to compare the quality of assemblies
by
GenoMax
141k
Are there any short read datasets available in SRA? Can you try and see how many left over reads remain after you align to both of your ass…
Comment: Korean human genome reference file
by
GenoMax
141k
From NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001712695.1/ Use the `Download` button or `curl/datasets`.
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
by
GenoMax
141k
> But it keeps giving error Please tell us what the error is.
Answer: 10x VDJ (TCR/BCR) BAM to fastq
by
GenoMax
141k
Looking at the information about the BAM file in the link included at the end of this sentence, it seems that the BAM file does not contain…
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