User: finswimmer77

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finswimmer7770
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Posts by finswimmer77

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Comment: C: Faster way to get coverage per base
... pileup.sh seems to need lot of memory which I have to little (around 6GB) :( The bed file is just needed to truncate the bam file to the region of interest. If I can pipe to pileup I can do this before with samtools view. So can I? Didn't find it in the documentation. fin swimmer ...
written 38 minutes ago by finswimmer7770
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Comment: C: Faster way to get coverage per base
... Should there be any reasonable differences to split the bam file and not the bed file with the regions of interests? I thought with the bam index it should be possible to have random access directly to the regions? fin swimmer ...
written 41 minutes ago by finswimmer7770
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Comment: C: Faster way to get coverage per base
... Never heard about sambamba before, but I will try it. fin swimmer ...
written 44 minutes ago by finswimmer7770
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Comment: C: Faster way to get coverage per base
... I'used bedtools before, but put it aside because of high memory usage (I just have have 6GB). But with the -sorted parameter it seemes to work at least with my small test dataset. I will will check it today on my large dataset. Thank you. fin swimmer ...
written 46 minutes ago by finswimmer7770
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Faster way to get coverage per base
... Hello, I would like to get the coverage for every single base in all regions in a bed file. For this I use samtools now `samtools depth -aa -b regions.bed input bam` This all works as excpected. But the more regions I have the longer this tasks takes of course. I can speed it up by dividing the b ...
alignment sam written 2 days ago by finswimmer7770 • updated 2 days ago by Vivek Todur30
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Comment: A: sam file error
... Hello, what was the exact command for producing your sam file? The lines with [M::mem_pestat] looks like info messages from bwa. But they should not appear in the sam file. fin swimmer ...
written 3 days ago by finswimmer7770
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Answer: A: Is it necessery to perform GATK-BQSR before performing variant calling using fre
... Hello, the authors of [freebayes][1] itself are saying, that neither BQSR nor VQSR is neccessary. fin swimmer [1]: https://github.com/ekg/freebayes#best-practices-and-design-philosophy ...
written 5 days ago by finswimmer7770
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Answer: A: How to merge multiple bam files into single bam file
... Hello, [samtools merge][1] can do this. fin swimmer [1]: http://www.htslib.org/doc/samtools.html ...
written 11 days ago by finswimmer7770
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Answer: A: VCF file period symbol in the genotype
... Hello, a period in a vcf file always means "no Data" or "unknown". So in your case at these sites the genotype for samples with ./. could not be determined. So you maybe take a look at the bam files why the variant calling failes here. Maybe the coverage is to low? fin swimmer ...
written 17 days ago by finswimmer7770
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Comment: C: Nextera and Trimmomatic
... Hello, > For Trimmomatic, I will use the paired end command so 4 files will be genereated (Forward_Paired, Forward_Unpaired, Reverse_Paired, Reverse_Unpaired). Which files should I choose for downstream analysis (Assembly and binning)? It depends. If you are only interesseted in high quality d ...
written 20 days ago by finswimmer7770

Latest awards to finswimmer77

Scholar 10 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file

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