User: mchaisso

gravatar for mchaisso
mchaisso160
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United States
Last seen:
3 years, 6 months ago
Joined:
6 years, 9 months ago
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Posts by mchaisso

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Help understanding the bam file generated from BLASR alignment
... For the second part, you make a file with the list of files to align in it, with the suffix of the file .fofn . -mark ...
written 3.5 years ago by mchaisso160
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Comment: C: Pacbio: extract fastq from h5 file based on quality filtering
... The quality values are sufficiently low that reads may be artificially trimmed by celera.  I've found it's best to just fake fastq from fasta with high enough quality value that reads are retained.  The assembly quality needs to be improved later using quiver. ...
written 4.6 years ago by mchaisso160
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Comment: C: Indel Discovery Delly, Pindel, Samtools, Gatk
... Is your data whole-genome or exome? PM-me if it is exome. ...
written 6.0 years ago by mchaisso160
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Answer: A: Pacbio Quiver Consensus - How To Use?
... Some notes: Quiver is typically used at the end of an assembly, after overlaying the reads back on the assembly with an alignment. If you are looking into ways to do hybrid assembly consider PacBioToCA http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA. If you are onl ...
written 6.3 years ago by mchaisso160
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Comment: C: Aligning Pacbio Reads
... The current version on github should have this fixed. E-mail me directly if not, and I'll fix it. -mark ...
written 6.6 years ago by mchaisso160
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Answer: A: Length Of Read Needed To Confidently Map Sequence
... I had to do a similar calculation for a recent paper. To break past the asymptotic line, the lengths of reads have to get much longer: http://www.biomedcentral.com/content/pdf/1471-2105-13-238.pdf (figure 6) ...
written 6.6 years ago by mchaisso160
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Answer: A: Aligning Pacbio Reads
... You can download blasr from github: https://github.com/PacificBiosciences/blasr . You need hdf5 installed to compile. Use default alignment parameters, but add the flag "-sam" to produce output in sam format if that is desired. -mark ...
written 6.7 years ago by mchaisso160
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Comment: C: Pacbio Rna-Seq Protocol
... Yup, that's my code, glad you like it. As always, the more the feedback the better. Blasr performs very poorly on spliced alignment. The introns violate some of the indel assumptions built into the code, and so you will often see part of a transcript mapped but many exons missing. I implemented s ...
written 6.7 years ago by mchaisso160
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Answer: A: Pacbio Rna-Seq Protocol
... I'm not sure about the sample preparation, but you can do alignment with GMAP. Contrary to popular belief, most (>95%) align properly without error correction with another platform. Fortunately, this is distributed across all genes (in the benchmarking I did) and so any isoform is usually detec ...
written 6.7 years ago by mchaisso160
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Comment: C: Quality Analysis Of Pacbio Data
... Hi, Every once in a while I ran into contamination problems. I created a blasr index of almost all prokaryotes, and just aligned to that (using blasr). The only caveat is I never updated blasr to allow for larger than 32 bit indexing, and so the largest database you can use is 4G. NCBI's set of ...
written 6.7 years ago by mchaisso160

Latest awards to mchaisso

Good Answer 4.6 years ago, created an answer that was upvoted at least 5 times. For A: Aligning Pacbio Reads
Appreciated 6.0 years ago, created a post with more than 5 votes. For A: Aligning Pacbio Reads
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Length Of Read Needed To Confidently Map Sequence
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Aligning Pacbio Reads

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