User: ATPoint

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ATPoint1.6k
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Be a computational biologist they said - it will be fun they said. 

Posts by ATPoint

<prev • 259 results • page 1 of 26 • next >
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Comment: C: Regarding Split reads and discordant reads
... > 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 ATPoint1.6k
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Comment: C: Remove mitochondrial reads from BAM files
... Check the number of reads per file, not the size, as it depends on the compression level. ...
written 1 day ago by ATPoint1.6k
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Comment: C: Remove mitochondrial reads from BAM files
... faster: mawk '($3 != "chrM" && $3 != "chrUn")' =) ...
written 1 day ago by ATPoint1.6k
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Comment: C: Build Bowtie2 2.3.3.1 with make on linux 64 bit
... Install libtbb-dev and retry. ...
written 3 days ago by ATPoint1.6k
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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 ATPoint1.6k
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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 ATPoint1.6k
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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 ATPoint1.6k
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Answer: A: Stranger Things: unexpected limitations of popular tools
... 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 ATPoint1.6k
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Comment: C: Genomic features of peaks at mature mRNA level
... 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 ATPoint1.6k
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Answer: C: question about the single-end sequencing
... 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 ATPoint1.6k

Latest awards to ATPoint

Student 7 days ago, asked a question with at least 3 up-votes. For Deeptools: computeMatrix - Traceback
Commentator 7 days ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Scholar 8 days ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Commentator 17 days ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Guru 4 weeks ago, received more than 100 upvotes.
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Centurion 9 weeks ago, created 100 posts.
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: To screen for a good aligner
Scholar 3 months ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Supporter 10 months ago, voted at least 25 times.
Student 11 months ago, asked a question with at least 3 up-votes. For Deeptools: computeMatrix - Traceback
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Scholar 13 months ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Scholar 16 months ago, created an answer that has been accepted. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Bedtools sortBed | uniq and bash sort | uniq returns different number of lines

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