User: Botond Sipos

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Botond Sipos1.6k
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United Kingdom
Website:
https://medium.com/@bo...
Twitter:
@boti_ka
Last seen:
15 hours ago
Joined:
7 years, 3 months ago
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Posts by Botond Sipos

<prev • 67 results • page 1 of 7 • next >
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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 4 months ago by Botond Sipos1.6k
0
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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 4 months ago by Botond Sipos1.6k
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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 6 months ago by Botond Sipos1.6k
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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 15 months ago by Botond Sipos1.6k
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 15 months ago by Botond Sipos1.6k
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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 15 months ago by Botond Sipos1.6k
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Comment: C: Conversion Of Blat Output To Sam/Bam
... I have tried a different approach: I have converted the PSL to BAM using the bamtools method above and cooked up a script to augment the BAM file with the sequences from the original fasta file. However the CIGAR string is inconsistent with the sequence length, for example: > Read 0 > R ...
written 15 months ago by Botond Sipos1.6k
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Comment: C: Conversion Of Blat Output To Sam/Bam
... It does not work unfortunately, the sequences are not included. Also the SAM output is invalid as there are often dashes in the CIGAR string like this: **2H-574M609H** ...
written 15 months ago by Botond Sipos1.6k
0
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Comment: C: Conversion Of Blat Output To Sam/Bam
... This works well, but is there a way to include the sequences in the generated SAM or one has to do that manually? ...
written 15 months ago by Botond Sipos1.6k
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Comment: C: How to make your snakefiles self-documenting
... Yeah, this might be a better way to do it :) ...
written 17 months ago by Botond Sipos1.6k

Latest awards to Botond Sipos

Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
Scholar 6 months ago, created an answer that has been accepted. For A: Fastx_toolkit with nanopore data
Autobiographer 18 months ago, has more than 80 characters in the information field of the user's profile.
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Help Make Biostar Better! Add Your Feedback, Opinions And Suggestions.
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Pacbio Rna-Seq Protocol
Guru 4.0 years ago, received more than 100 upvotes.
Voter 4.0 years ago, voted more than 100 times.
Supporter 4.0 years ago, voted at least 25 times.
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Rnaseq Simulation: What To Set Number Of Fragments To When Using `Rlsim`
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Kaks Calculator
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Rlsim, A Package For Simulating Rna-Seq Library Preparation With Parameter Estimation
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Review Papers On Short Read Mapping?
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