User: peri.tobias

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Posts by peri.tobias

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Comment: C: BWA-MEM using long PacBio reads
... thanks, appreciated! ...
written 4 months ago by peri.tobias0
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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 4 months ago by peri.tobias0
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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 4 months ago by peri.tobias0
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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 4 months ago by peri.tobias0
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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 4 months ago by peri.tobias0
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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 4 months ago by peri.tobias0
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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 4 months ago by peri.tobias0
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nucleotide Hidden Markov Model search
... I am using HMMER v3.1 for nucleotide Hidden Markov Model searches. What I can't find in the manual is whether the hmm (I am building species-specific domain specific hmm) used to search a database looks at the plus and minus strand of the sequences in the database. To clarify - when running a BLAS ...
nhmmer hmmer written 21 months ago by peri.tobias0 • updated 20 months ago by Biostar ♦♦ 20
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Comment: C: Making bed files from fasta
... Thanks Matt. Yes I should have looked a bit closer before posting. ...
written 2.1 years ago by peri.tobias0
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Answer: A: Making bed files from fasta
... My apologies, my biopython script was corrupted. The fasta is okay. ...
written 2.1 years ago by peri.tobias0

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Popular Question 13 months ago, created a question with more than 1,000 views. For Making bed files from fasta
Scholar 2.1 years ago, created an answer that has been accepted. For A: Making bed files from fasta

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