User: peri.tobias

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peri.tobias10
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Posts by peri.tobias

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Comment: C: Alternative to BLASR ?
... Yes, you are correct. I should have been clearer. This is the script I used. minimap2 -ax map-pb genome.fasta *.fastq \ | samtools view -hF 256 - \ | samtools sort -@ 8 -o genome_aligned.bam I should also say that I am still having some trouble with pbbamify. So I haven't got this whole step wor ...
written 5 days ago by peri.tobias10
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Comment: C: Alternative to BLASR ?
... Hello and thanks for all these suggestions. These further comments might help someone else. I have used minimap2 to map PacBio raw reads (converted to fastq as required for minimap2) against my de novo assembly. I recommend this approach over blasr. Use samtools to get the aligned.bam. Minimap2 doe ...
written 7 days ago by peri.tobias10
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inputs to genomicconsensus arrow algorithm
... Firstly apologies, this is a cross-post from here as I was not sure if I had sent to the correct forum. If I get a useful answer I will make sure it is across both platforms. https://github.com/PacificBiosciences/pbcore/issues/118 I have assembled a de novo genome (1.98 Gb) with canu v1.6 using pa ...
assembly polish arrow pacbio written 7 weeks ago by peri.tobias10
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Comment: C: BWA-MEM using long PacBio reads
... thanks, appreciated! ...
written 10 months ago by peri.tobias10
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Comment: C: BWA-MEM using long PacBio reads
... Thanks very much for your comment, genomax. I initially used dextract to output fasta, quiver and arrow files from bam and hdf5. https://dazzlerblog.wordpress.com/tag/arrow/ Quiver files are fastq-like but not exactly fastq format - though a simple conversion is probably possible. I intend to polis ...
written 10 months ago by peri.tobias10
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Comment: C: BWA-MEM using long PacBio reads
... Just wanted to add that bbmap only seems able to take one in=file. My above trials at listing files does not work. Perhaps you could concatenate but my fasta files are huge so not going to risk. Will run them individually and output multiple unmapped and mapped .fasta files. ...
written 10 months ago by peri.tobias10
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Comment: C: BWA-MEM using long PacBio reads
... another way to list all the fasta files is: mapPacBio.sh in=`echo ./foo/*.fasta` outu=unmapped.fasta outm=mapped.fasta maxlen=6000 ...
written 10 months ago by peri.tobias10
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Comment: C: BWA-MEM using long PacBio reads
... The above script does not work. For mutiple fasta inputs you need to list them all. *.fasta is not recognised. The following seems to work. bbmap.sh ref=AP_MT.fa mapPacBio.sh in=reads1.fasta reads2.fasta reads3.fasta outu=unmapped.fasta outm=mapped.fasta maxlen=6000 ...
written 10 months ago by peri.tobias10
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Comment: C: BWA-MEM using long PacBio reads
... Thanks, I saw this in the manual. What I am unclear about is the inputs. I will try this to see how it runs: bbmap.sh ref=AP_MT.fa bbmap/mapPacBio.sh in=/project/Assembly/*.fasta outu=unmapped.fasta outm=mapped.fasta ref=AP_MT.fa maxlen=6000 ...
written 10 months ago by peri.tobias10
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Comment: C: BWA-MEM using long PacBio reads
... Hello all, I know that this is an old thread but I have a large amount of raw PacBio reads that I wish to map to an existing mitochondrial sequence (only 90kbp) to extract unmapped reads to use in assembly. Can I use the above script with bbmap? I can't find this usage in the manual. It seems to t ...
written 10 months ago by peri.tobias10

Latest awards to peri.tobias

Popular Question 5 months ago, created a question with more than 1,000 views. For Making bed files from fasta
Popular Question 19 months ago, created a question with more than 1,000 views. For Making bed files from fasta
Scholar 2.6 years ago, created an answer that has been accepted. For A: Making bed files from fasta

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