User: peri.tobias

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peri.tobias10
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Posts by peri.tobias

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Why is the pacbio bam 10X the original bam file size?
... Running the genomicconsensus arrow on aligned raw reads against a de novo pacbio assembly (1 Gbase assembly). Used minimap2 for the aligned.bam and then pbbamify to format for use with arrow. Can't find information on what this reformatting does but the initial aligned.bam = 35G and the pb_align ...
arrow pbbamify genomicconsensus pacbio written 10 weeks ago by peri.tobias10
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Comment: C: Alternative to BLASR ?
... Thanks for these tips @harish. I did not know that I could directly use subreads with Pbmm2. Actually this all looks more promising as a way forward. Pbbamify worked after 130 hours of walltime. It output a very large pb.bam (351G) from aligned.bam (36G). Arrow still needs a pbi indexed file accord ...
written 3 months ago by peri.tobias10
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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 3 months 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 3 months 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 4 months ago by peri.tobias10
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Comment: C: BWA-MEM using long PacBio reads
... thanks, appreciated! ...
written 13 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 13 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 13 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 13 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 13 months ago by peri.tobias10

Latest awards to peri.tobias

Popular Question 8 months ago, created a question with more than 1,000 views. For Making bed files from fasta
Popular Question 22 months ago, created a question with more than 1,000 views. For Making bed files from fasta
Scholar 2.9 years ago, created an answer that has been accepted. For A: Making bed files from fasta

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