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Recent Replies
Comment: Transform Data into DNA picture
by
anasjamshed1994
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120
How can I annotate with mutations?
Comment: open-cravat: variant annotation tool
by
allison_cox
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0
Hello,
I am trying to use open-cravat to add annotations to vcf files. I have set up a venv, activated, installed open-cravat, installed th…
Comment: Automated way to pull representative/RefSeq genome using full species name?
by
GenoMax
123k
Download using accession numbers : https://www.biostars.org/p/9544394/#9545941
Comment: Automated way to pull representative/RefSeq genome using full species name?
by
predeus
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1.8k
Hi Mirian,
Thank you for your comment! I wanted to maybe avoid downloading all the bacterial species, and only download the assemblies an…
Comment: Transform Data into DNA picture
by
anasjamshed1994
▴
120
what does genotype mean in rsid? What does it indicate?![rsid][1]
[1]: /media/images/7638ed2f-7ed2-4cc0-8ce4-58ab0226
Comment: Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me
by
hiroyuki.kato.911
•
0
Thanks! I got it!
Answer: Inquiry related to processing multiple db file simulataneously
by
Pierre Lindenbaum
151k
how about calling `dbDisconnect` after `dbGetQuery` ?
Answer: Automated way to pull representative/RefSeq genome using full species name?
by
MirianT_NCBI
▴
340
Hi Alex,
You can use [NCBI Datasets][1]. `datasets` allows users to download genome and associated annotation files as a data package. I…
Comment: bedtools getfasta error: Error: malformed GFF entry at line 15. Coordinate detec
by
Pierre Lindenbaum
151k
but it's decoded AS a GFF/GTF file because bedtools can see columns 4 and 5 are integers. move columns 4 and 5 to columns 2 and 3 to create…
Comment: BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene
by
Matthias Zepper
2.4k
I already linked the MANE website above. Navigate to *Accessing MANE data* and download [this file][1]. It is an equivalence table and cont…
Comment: bedtools getfasta error: Error: malformed GFF entry at line 15. Coordinate detec
by
Simone
•
0
It's not a GFF file, it's a TSV annotation file, output from BUSCO. The annotations are coordinates for BUSCO genes. I've tried using BEDOP…
Comment: What are Supplementary Reads?
by
cmdcolin
★
2.5k
Large insertions or deletions can cause supplementary alignments to be created, even though it is still linear. But, minimap2 will try to a…
Comment: How to find rna strand direction before alignment?
by
swbarnes2
12k
OP said he didn't want to align. That script takes a bad and a bam as input.
Comment: GO enrichment analysis graphs after goseq: any easy solutions?
by
afsanarupa1
•
0
Please can you tell me details step by step how can these types of graphs be generated using output files from goseq as stated in trinity p…
Comment: What's Supplementary Reads?
by
Istvan Albert
96k
one concept the "linearity" of the alignment is important. A chimeric alignment is found to be "chimeric" if the entire read is represented…
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