User: aostern

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aostern30
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Posts by aostern

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Comment: C: Weird BWA MEM Behavior: Zero-Length Read
... Do you think there's a way to salvage the SAM I have? Or do I need to fix the FASTQs and then realign them? ...
written 14 months ago by aostern30
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Comment: C: Weird BWA MEM Behavior: Zero-Length Read
... Huh, you're right. I guess I'm somehow using `fastq-dump` wrong. All my FASTQs start like that. `head *.fastq`: ==> SRR1514950.fastq <== Read 216120040 spots for SRR1514950.sra Written 216120040 spots for SRR1514950.sra NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ...
written 14 months ago by aostern30
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Comment: C: Weird BWA MEM Behavior: Zero-Length Read
... `all.fastq` is 342G. For each of three `.sra` files, I did `fastq-dump SRR1514950.sra > SRR1514950.fastq` `head all.fastq`: Read 216120040 spots for SRR1514950.sra Written 216120040 spots for SRR1514950.sra NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ...
written 14 months ago by aostern30
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Weird BWA MEM Behavior: Zero-Length Read
... I tried to use BWA MEM to map reads from an interleaved FASTQ. fastq="all.fastq" fasta="/share/PI/apps/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa" bwa="/share/PI/apps/bcbio/anaconda/bin/bwa" nThreads="12" #Run BWA MEM #IMPORTANT: NEED -p since "$fastq" is an interleav ...
genome software error alignment sequencing written 14 months ago by aostern30 • updated 14 months ago by h.mon27k
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Answer: A: pysam pileup: what reads appear in the pileup?
... Cross-posted on Bioinformatics.SE. I hope that's OK. Answer was provided there. Short version: pysam pileup() just wraps samtools mpileup, and mpileup by default filters out reads not just with a base quality—but also with a "base alignment quality"—lower than 13. ...
written 14 months ago by aostern30
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pysam pileup: what reads appear in the pileup?
... [Cross-posted][1] on Bioinformatics.SE. I hope that's OK. **Answer was provided there.** Short version: pysam `pileup()` just wraps samtools `mpileup`, and `mpileup` by default filters out reads not just with a base quality—but also with a "*base alignment quality*"—lower than 13. ______ I thought ...
software genome alignment pysam sequencing written 15 months ago by aostern30
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Comment: C: Determine Insertion Sequence
... Sounds good. Thanks! Have you heard of Pamir ([https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870608/][1]), btw? [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870608/ ...
written 17 months ago by aostern30 • updated 17 months ago by h.mon27k
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Comment: C: Determine Insertion Sequence
... Thanks for the quick response! GRIDSS looks pretty cool—I think I'll try it! Just to be clear, what information (out of position, length, nucleotide content) does it report on insertions, and for what sizes? ...
written 17 months ago by aostern30
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Comment: C: Determine Insertion Sequence
... Thanks for the quick response. It sounds like most tools are pretty limited in the size of the insertions they can find the content of. ...
written 17 months ago by aostern30
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Determine Insertion Sequence
... Hi guys, I've developed a tool that identifies the points at which insertions are made. This basically means, for various BAM files, I have various lists of coordinates at which I think insertions were made with various degrees of confidence. I'm trying to detect indels with sizes from around 10bp ...
indel assembly alignment sv sequencing written 17 months ago by aostern30 • updated 17 months ago by d-cameron2.1k

Latest awards to aostern

Scholar 14 months ago, created an answer that has been accepted. For A: pysam pileup: what reads appear in the pileup?

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