User: ATPoint
ATPoint • 1.6k
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Be a computational biologist they said - it will be fun they said.
Posts by ATPoint
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... > insert size of my libaray dataset is 1.5 kb
What kind of library prep and sequencing platform were used for the experiment? 1.5kb is pretty big. Also, if you want to detect structural variants, such as deletions, I highly recommend using established tools, such as VarScan2, Freebayes, VarDict. ...
written 1 day ago by
ATPoint • 1.6k
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... Check the number of reads per file, not the size, as it depends on the compression level. ...
written 1 day ago by
ATPoint • 1.6k
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... faster:
mawk '($3 != "chrM" && $3 != "chrUn")'
=)
...
written 1 day ago by
ATPoint • 1.6k
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... Install libtbb-dev and retry. ...
written 3 days ago by
ATPoint • 1.6k
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Comment:
C: Deseq2 count matrix
... You do not need to. DESeq2 has an internal data-driven function to exclude low counts. There are many questions/posts about this topic on Bioconductor, just google around a bit. ...
written 3 days ago by
ATPoint • 1.6k
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Comment:
C: bedtools multicov problem
... Can you post a subset of the BED file. I would guess that either the BED has "*" or "." in the strand column or no strand column at all. Therefore, neither "+", nor "-" would be specified and your result. ...
written 3 days ago by
ATPoint • 1.6k
2
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Comment:
C: Picard tools duplicate removal
... Hope you do not want to remove duplicates from RNA-seq data, as the tags of your post suggest? ...
written 3 days ago by
ATPoint • 1.6k
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... It does not relate to a certain tool, but why are databases like dbGaP, IHEC and DEEP access restricted, requiring to fill out these extensive application forms, including abstracts of your project. It is not that these databases contain manuals to build biological weapons, so why all this restricti ...
written 4 days ago by
ATPoint • 1.6k
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1
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... What kind of peaks are this? You talk about genomic regions but provide transcriptomic features you want to map to. Please specify what your goal is. ...
written 4 days ago by
ATPoint • 1.6k
2
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1
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... Check the [Illumina video][1] at about 1:40min. During cluster generation both strands are present, but one strand is washed away prior to sequencing. In single-end mode, this remaining strand is sequenced. In paired-end, after the readout of the first strand is finished, this one is bridge-amplifie ...
written 5 days ago by
ATPoint • 1.6k
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For Deeptools: computeMatrix - Traceback
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For C: To screen for a good aligner
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For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
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received more than 100 upvotes.
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For C: To screen for a good aligner
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