User: O.rka

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O.rka70
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Posts by O.rka

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Comment: C: How to map RNA-seq with hisat2, stringtie, an assembly fasta, a gtf file, and a
... Thanks, this is really helpful. So I would do: # Set up the exons/splice sites `hisat2_extract_splice_sites.py annotation.gtf > splicesites.tsv` `hisat2_extract_exons.py annotation.gtf > exons.tsv` # Build index `hisat2-build --ss ./splicesites.tsv --exon ./exons.tsv assembly.fa organism_A` ...
written 6 days ago by O.rka70
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How to map RNA-seq with hisat2, stringtie, an assembly fasta, a gtf file, and a transcript fasta?
... I have the following files: assembly.fa transcripts.fa annotation.gtf My organism is eukaryotic with introns so I was to use the hisat2 -> stringtie pipeline. The example in the below link looks like it maps to the chromosomes/assembly and not the transcripts with HISAT2. If there were introns ...
stringtie hisat2 mapping transcriptome written 6 days ago by O.rka70 • updated 6 days ago by swbarnes24.7k
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Answer: A: Which Ensembl chromosome sequence file is used for the gff3 files?
... Note for anyone trying to do this in the future. From the answers and very helpful conversation above, I got this combination to work: ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz ftp://ftp.ensembl.org/pub/grch37/current/gff3/h ...
written 28 days ago by O.rka70
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Comment: C: Which Ensembl chromosome sequence file is used for the gff3 files?
... Which version/ftp-link do you recommend for me to get the chromosome sequences? The one I used was: ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz and it appeared to have only Ns for all of the chromosomes. Thank you. ...
written 4 weeks ago by O.rka70
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Comment: C: Which Ensembl chromosome sequence file is used for the gff3 files?
... Thank you! The part that was confusing for me is that when I looked at the coordinates of GFF3 file in comparison to the DNA toplevel fasta and all the exon sections were N. ...
written 4 weeks ago by O.rka70
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Which Ensembl chromosome sequence file is used for the gff3 files?
... **I can't which of the following files were used to create the GFF3 files?** ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz or an ...
gff3 ensembl genome human chromosome written 4 weeks ago by O.rka70
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Comment: C: How to download all premRNA sequences (exons + introns) for human GRCh38 with En
... Any way to make the script I have above quicker? It's going to take forever for hg19: 1%| | 1226/104763 [54:47<192:16:23, 6.69s/it] ...
written 4 weeks ago by O.rka70
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How to download all premRNA sequences (exons + introns) for human GRCh38 with Ensembl IDs?
... I'm not seeing anything on the FTP website that has this info: ftp://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/ My main goal is to get the exons in uppercase and the introns in lowercase. I tried using this but it dot work for many of the identifiers and takes a long time: # Download ...
ensembl database rna-seq human sequences written 5 weeks ago by O.rka70 • updated 29 days ago by Biostar ♦♦ 20
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Comment: C: Where can I download ALL pfam flat-file annotations?
... I essentially want to get the name and description given a pfam identifier. For example, `'PF01565': {'NAME': 'FAD_binding_4', 'DESCRIPTION': 'FAD binding domain'}` ...
written 8 weeks ago by O.rka70
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Comment: C: Where can I download ALL pfam flat-file annotations?
... I only found one file with annotations ^^^. Do you know if there is another file on the ftp site? ...
written 8 weeks ago by O.rka70

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Popular Question 28 days ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 3 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Scholar 3 months ago, created an answer that has been accepted. For A: Can you assemble with merged paired end reads and unmatched reads as "single end
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Popular Question 5 months ago, created a question with more than 1,000 views. For Most up-to-date Gene Ontology [GO] analysis?
Great Question 8 months ago, created a question with more than 5,000 views. For How to tell bloodtype from SNPs data?
Popular Question 9 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
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