User: ibseq12

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ibseq120
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Posts by ibseq12

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Answer: A: Open source alternatives to SureCell RNA Single-Cell App in Basespace?
... ddseeker at https://github.com/cgplab/ddSeeker ...
written 12 days ago by ibseq120
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Answer: A: How To Filter Mapped Reads With Samtools
... does the below apply to single end sequencing data? samtools view -b -F 4 -f 8 file.bam > onlyThisEndMapped.bam samtools view -b -F 8 -f 4 file.bam > onlyThatEndMapped.bam samtools view -b -F12 file.bam > bothEndsMapped.bam samtools merge merged.bam onlyThisEndMapped.bam onlyThatEndMapped ...
written 5 weeks ago by ibseq120
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Comment: C: How To Filter Mapped Reads With Samtools
... does the below apply to single end sequencing data? samtools view -b -F 4 -f 8 file.bam > onlyThisEndMapped.bam samtools view -b -F 8 -f 4 file.bam > onlyThatEndMapped.bam samtools view -b -F12 file.bam > bothEndsMapped.bam samtools merge merged.bam onlyThisEndMapped.bam onlyThatEndMapped.b ...
written 6 weeks ago by ibseq120
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bwa mem -w option
... does anybody know what is the range of INT that can be used for the -w option of BWA Mem? (-w ) : INT*Band width. Essentially, gaps longer than *INT* will not be found. Note that the maximum gap length is also affected by the scoring matrix and the hit length, not solely determined by this option. ...
assembly written 15 months ago by ibseq120
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Comment: A: Working example for VCF visualization in Circos
... hi genebow any more thoughts? did you manage to use circos for snp? ...
written 17 months ago by ibseq120
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Comment: C: Pca From Vcf Files
... which version if R can be ran into? I got this error: > library("SNPRelate") Error in library("SNPRelate") : there is no package called ‘SNPRelate’ > install.packages("SNPRelate") Installing package into ‘/Users/ib7/Library/R/3.4/library’ (as ‘lib’ is unspecified) Warning in install.packages ...
written 20 months ago by ibseq120
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Answer: A: Homozygous Indel/Snp & Heterozygous Indel/Snp
... Hi just confused about this: AAATTTGGGCTTTAAA - Reference genome (Chr 1) AAATTTGGGtTTTAAA - Non-reference genome (Chr 1 from father) AAATTTGGGtTTTAAA - Non-reference genome (Chr 1 from mother) why we don't info about the biallelic site on the reference genome - is it homo or heterozygous? E.g. co ...
written 2.0 years ago by ibseq120

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