User: curiousbiologist

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Location:
France
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Posts by curiousbiologist

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Which strategy to get draft genome: rawread mapping or de novo assembly?
... thank you Fabio! very usefull ...
written 4 weeks ago by curiousbiologist30
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Which strategy to get draft genome: rawread mapping or de novo assembly?
... Hi all, I want to generate a clean consensus genome from fastq files. I also have a close reference I would like your opinion about what is the best strategy to get a draft genome: I can't determine from bibliography the best strategy: rawread mapping or de novo assembly? or both? Is there a refer ...
consensus assembly genome written 4 weeks ago by curiousbiologist30
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Comment: C: generation of sequences (from bam) starting at a specific position
... Yes you got it [genomax2][1]. I want to have several (and switchable) windows of reads from different samples in order to compare them using different score calculations; stats, entropy ([https://www.biostars.org/p/223824/][2]). If I haven't same size of reads pieces, my results will be misrepresent ...
written 9 months ago by curiousbiologist30
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Comment: C: generation of sequences (from bam) starting at a specific position
... Thank you for your answer, it means to me to have a return. My programming skills are not great, do you know a script that I can use as start basis to do my custom script? ...
written 9 months ago by curiousbiologist30
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Answer: A: generation of sequences (from bam) starting at a specific position
... would it be possible to resolve this problem using an awk script? I was thinking of an alignment, conversion to fasta (with gap or x for non-aligned bases) and then trimming using awk or fastx_trimmer? Maybe there is something easier? how do I get gap or 'x' for non-aligned bases before and after ea ...
written 9 months ago by curiousbiologist30
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Comment: C: generation of sequences (from bam) starting at a specific position
... Thank you for your answer! However, I got reads matching within the interval given, not cropped reads inside this interval ...
written 9 months ago by curiousbiologist30
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Answer: A: generation of sequences (from bam) starting at a specific position
... I'm deeply sorry if my question was obscure: what I want to do is to get, from an alignment, reads without nucleic bases before position 30 of the reference sequence. Is it possible to crop a bam file? ...
written 9 months ago by curiousbiologist30
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Comment: C: generation of sequences (from bam) starting at a specific position
... I would like to play with all the selected reads after, I'm not sure consensus is a good approach ...
written 9 months ago by curiousbiologist30
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Comment: C: generation of sequences (from bam) starting at a specific position
... I would like to obtain a bam "cropped" (all my reads aligned and starting at a defined position) ...
written 9 months ago by curiousbiologist30
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generation of sequences (from bam) starting at a specific position
... How can I generate sequences from a bam/sam file starting at a specific position and remove what is before this position? Thank you! ...
alignment sequence written 9 months ago by curiousbiologist30

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