User: Maximilian Haeussler

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UCSC
Website:
http://genome.ucsc.edu/
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7 months ago
Joined:
8 years, 1 month ago
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m**********@gmail.com

Posts by Maximilian Haeussler

<prev • 104 results • page 1 of 11 • next >
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Comment: C: Stranger Things: unexpected limitations of popular tools
... The UCSC bigBed format is something that comes very close: it has only very few defined minimal columns (chrom, start, end, score, strand) and you can add what you want. If the file has a certain structure, it's a PSL (called bigPsl) alignment. It can also be a gene model file when it has certain co ...
written 7 months ago by Maximilian Haeussler1.3k
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Answer: A: BWASW and _alt alleles
... So the answer seems to be (see comments above): bwa-sw does not support the XA tag. As such, you cannot get the alternative locations for multi-mapping sequences. This makes bwasw quite useless for most real-world applications that I can imagine, tasks that do not involve mapping reads to a genome. ...
written 8 months ago by Maximilian Haeussler1.3k
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Comment: C: BWASW and _alt alleles
... In this case, my input sequence can be <= 3000 bp.... but you're right, maybe I should use BWA-mem for this? I used bwasw because the input is pretty long, by BWAMEM standards. ...
written 8 months ago by Maximilian Haeussler1.3k
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Comment: C: BWASW and _alt alleles
... Oh wow, yes, it's indeed there, just not documented under bwasw but bwa backtrack: "Repetitive hits will be randomly chosen." manytThanks!! Well, yeah, I need to know the best match for the input sequence and the _alt match is definitely not a very useful match. I thought that BWA knew better these ...
written 8 months ago by Maximilian Haeussler1.3k
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BWASW and _alt alleles
... BWA-SW does not find all matches for me, it seems to pick only one random best match. I have no idea how to modify the arguments to have BWA find the secondary matches. Example: temp.fa: >hg38-chr6-test AACACAGGCCGGACAGAAGCTTGGAAGGTCCTGTCTCCCCAGGGAGGAGGCCCCTGGGACAGTGTGGCTCGTGTCCTTCC ...
alignment bwa blat written 8 months ago by Maximilian Haeussler1.3k
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Comment: C: UCSC MySQL query to find gene symbols for all RefSeq IDs?
... If you have RefSeq IDs to map to something else, I would use the NCBI efetch tools, as Pierre Lindenbaum suggests above. I would never use a third party webservice for a pipeline you want to run again. ...
written 11 months ago by Maximilian Haeussler1.3k
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Comment: C: Running Bowtie As Service Or Daemon?
... On our server, Centos 6.8, the -shmem option hangs. I got around that by putting the index into /dev/shm and using --mm, which should be the same thing. ...
written 15 months ago by Maximilian Haeussler1.3k
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Comment: C: Running Bowtie As Service Or Daemon?
... In a more current bowtie2 version, this exists now. ...
written 15 months ago by Maximilian Haeussler1.3k
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Answer: A: BWA shm index preloading: only for BWA MEM?
... I read over the BWA source code and figured that yes, only "bwa mem" can use the mmaped index, "bwa aln" cannot. bowtie1 and bowtie2 both can use the mmap'ed index. Note that there is a github issue in the bwa repo on github where users report a 25% performance drop when using this option, so YMMY. ...
written 15 months ago by Maximilian Haeussler1.3k
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Comment: C: Is there an open version of f1000
... Argh!! I was confused, sorry. Yes, I meant F1000prime. I wonder if many of their customers understand the difference between their products... ...
written 15 months ago by Maximilian Haeussler1.3k

Latest awards to Maximilian Haeussler

Centurion 8 months ago, created 100 posts.
Popular Question 10 months ago, created a question with more than 1,000 views. For BWA shm index preloading: only for BWA MEM?
Appreciated 15 months ago, created a post with more than 5 votes. For A: Drawing Chromosome Ideogams With Data
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Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Drawing Chromosome Ideogams With Data
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