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Answer: How to generate a .sam/.bam file of a particular chromosome or even a particular
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```samtools view -b in.bam chr1:100000-200000 > out.bam``` did not work for me.
But ```samtools view -b in.bam 1:100000-200000 > out.bam``…
Answer: Would this laptop be sufficient for small dataset/sequence analysis?
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1. I agree that 16 Gb RAM is probably not enough. **Buy as much RAM as you can afford**, even at the expense of disk space. Disk is cheap…
Comment: inquiry related to snpsift
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I use the above command as mentioned by you. the commands:
bcftools annotate -x ID file_chr2.vcf
the error: [W::bcf_hdr_check_sanit…
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I actually just added one part of the input file.
8,-0.48:0.150:.:. 0|0:-0.48,-0.48,-0.48:0.200:.:. 0|0:-0.48,-0.48,-0.48:0.350:.:. 0|0:-0.…
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16 GB of RAM will not cut it for any serious bioinformatics application these days. Doubly so if you choose to run Windows.
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I see - thanks. I am not sure that `SnpSift annotate` can do this, but you can first remove the original ID via `bcftools`, as follows:
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South Africa? - very nice. I had been considering moving there, would you believe.
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the command:
java -jar SnpSift.jar annotate dbSnp144.vcf variants.vcf > variants_annotated.vcf
I am getting no error.
the input file …
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Hi there, just to follow up on this, I used your package to generate my volcano plots and got exactly what I was looking for. I now wish to…
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Hi, please show:
1. the command(s) that you are using
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4. any status, wa…
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thanks GenoMax I will try this sorry for delay in reply!!
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The alternative, constant off-by-one errors, aren't my idea of fun either :-)
Comment: Removing genes of Seurat object during integration pipeline
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Stevens
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Yeah, you can filter min_cells in Seurat with SCtransform. That would probably change the gene numbers in the SCT assay of the object. I u…
Comment: Removing genes of Seurat object during integration pipeline
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ATpoint
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Doesn't sctransform has a `min_cells` parameter that you could use here? It will only consider genes detected in at least `min_cells` cells…
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Stevens
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I was thinking of making it an arbitrary cut off of 10 cells, Seurat's documentation uses 3 for reading in a single sample. I believe that …
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