User: Botond Sipos

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Botond Sipos1.7k
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Location:
United Kingdom
Website:
https://medium.com/@bo...
Twitter:
@boti_ka
Last seen:
2 hours ago
Joined:
7 years, 10 months ago
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Posts by Botond Sipos

<prev • 71 results • page 1 of 8 • next >
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Tool: pinfish: tools to annotate genomes using long read transcriptomics data
... [Pinfish](https://github.com/nanoporetech/pinfish) is a collection of tools helping to make sense of long transcriptomics data (long cDNA reads, direct RNA reads). The toolchain is composed of the following tools: - `spliced_bam2gff` - a tool for converting sorted BAM files containing spliced align ...
nanopore tool annotation isofrom rna-seq cdna written 28 days ago by Botond Sipos1.7k
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Answer: A: On the usage of Golang
... I have built some bioinformatics tools in Go, and my opinion is that it is very much worth learning. Probably the best thing about it that it truly follows the zen of Python principle that "There should be one-- and preferably only one --obvious way to do it." :) Hence it is a small language, but it ...
written 6 weeks ago by Botond Sipos1.7k
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Comment: C: D. melanogaster transposable elements in Ensembl/Flybase annotations
... I have contacted FlyBase regarding this and indeed the expressed TEs are not part of the gene annotation. ...
written 6 weeks ago by Botond Sipos1.7k
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D. melanogaster transposable elements in Ensembl/Flybase annotations
... Does anybody know if expressed transposable elements are included in the Ensembl/Flybase D. melanogaster gene annotations? ...
ensembl transposon annotation written 6 weeks ago by Botond Sipos1.7k
4
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Answer: A: BAM file comparison
... The [wub][1] package has a [script][2] for comparing BAM files. It does a coarse comparison of alignments (checks whether the start position of the alignments is close enough) and also calculates a "consistency score" (the fraction of bases which align the same way). The package also has a simple [ ...
written 11 months ago by Botond Sipos1.7k
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Comment: C: simulate rnaseq reads from ref. genome
... [Gffread][1] can extract the transcripts for you. [1]: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread_ex ...
written 11 months ago by Botond Sipos1.7k
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Tutorial: A gentle introduction to biogo
... I wrote two introductory posts on [bíogo][1], the bioinformatics library for [Golang][2]: [part I][3] [part II][4] [1]: https://github.com/biogo/biogo [2]: https://golang.org/ [3]: https://medium.com/@boti_ka/a-gentle-introduction-to-b%C3%ADogo-part-i-65dbd40e31d4 [4]: https://medium.com/@ ...
golang tutorial sequence biogo written 12 months ago by Botond Sipos1.7k
1
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Answer: A: Fastx_toolkit with nanopore data
... You can easily do that conversion using biopython: from Bio import SeqIO count = SeqIO.convert("input.fastq", "fastq", "output.fasta", "fasta") print("Converted %i records" % count) ...
written 22 months ago by Botond Sipos1.7k
1
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Answer: A: Conversion Of Blat Output To Sam/Bam
... I wrote a conversion tool in Python: https://www.biostars.org/p/233308/ ...
written 22 months ago by Botond Sipos1.7k
2
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0
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833
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Tool: Uncle PSL: BLAT to SAM conversion in Python
... [https://github.com/bsipos/uncle_psl][1] The package performs conversion of BLAT output ([PSL][2]) to [SAM][3] format. If the -N option is used then deletions larger than the specified limit are represented by the N CIGAR operation. Conversion was tested on simulated reads against output generated ...
alignment blat tool rna-seq sam written 22 months ago by Botond Sipos1.7k

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Appreciated 15 days ago, created a post with more than 5 votes. For A: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
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Scholar 12 months ago, created an answer that has been accepted. For A: Fastx_toolkit with nanopore data
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Appreciated 3.6 years ago, created a post with more than 5 votes. For A: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Pacbio Rna-Seq Protocol
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