Moderator: ATpoint

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ATpoint31k
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Germany
Last seen:
17 minutes ago
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3 years, 11 months ago
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PhD Student Genomics (Wetlab/Drylab) {^Enter|fancy|buzzwords$}

Posts by ATpoint

<prev • 4,553 results • page 2 of 456 • next >
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Comment: C: Error using makeGRangesFromDataFrame in an R workflow for ATAC-seq
... Can you try again with `makeGRangesFromDataFrame(data.frame(atac_esca), keep.extra.columns = TRUE)`? Looks like this is not a standard data frame but a mixture of several other classes. ...
written 5 hours ago by ATpoint31k
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Comment: C: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
... I think it is the same. ENA also writes files to a temporary file name unless everything is properly finished. If you get a final fastq file like `.fastq.gz` it should be ok. ...
written 5 hours ago by ATpoint31k
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Comment: C: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
... Yes, only `--split-3` and `--gzip` are sratools options from `fastq-dump`. `parallel-fastq-dump -h` explains what the others are. In my experience when the download completed successfully, and only then, you will have a *.sra file on your disk. If anything goes wrong then `prefetch` does not conve ...
written 6 hours ago by ATpoint31k
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Comment: C: Filter out supplementary aligned reads for variant calling or not
... If you later during analysis of the results see that something is wrong you can still dig deeper if supp. alns might be a factor but I doubt so. I learned over the years that one should not overthink things and only start to debug if there is evidence for something going wrong. It might cost a lot o ...
written 6 hours ago by ATpoint31k
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Comment: C: Extract quality scores from aligned BAM files
... From all the quality assessments you can make in ChIP-seq MAPQ is probably the one that is least meaningful. You should take all reads that are above a reasonable threshold like 20 and then call peaks, check fractions of reads per peaks and produce bigwigs to check data on a browser track. This is w ...
written 7 hours ago by ATpoint31k
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Answer: C: Error using makeGRangesFromDataFrame in an R workflow for ATAC-seq
... Output of `packageVersion("GenomicRanges")`, `head(atac_esca)` and `class(atac_esca)`? Never seen this error message and I use this function like every day. Could be Windows-related or your data frame is in fact not a df but a different class like any of these dplyr formats. I also suggest to never ...
written 7 hours ago by ATpoint31k
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Comment: C: Failed to run Bismark tool on fasta file
... This is the answer field, and it is for answers. Please use `add comment` or `add reply` ...
written 7 hours ago by ATpoint31k
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Answer: A: Exonerate installation on server
... Conda: https://anaconda.org/bioconda/exonerate Binaries and source package: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate The README of the souce package contains `How do I build exonerate ?` which you should read. ...
written 8 hours ago by ATpoint31k
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Comment: C: Machine learning Algorithms on DNA sequences
... With respect, if you do not even know where to start and if this even will be helpful then maybe are more well-defined project might make sense and most importantly => an experienced supervisor is required. ...
written 10 hours ago by ATpoint31k
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Comment: C: parallel bwa mem with compressed fastq.bz2 files
... Yes, that is possible, see also https://sourceforge.net/p/bio-bwa/mailman/bio-bwa-help/thread/512E3D0C.1030807@bcgsc.ca/ ...
written 11 hours ago by ATpoint31k

Latest awards to ATpoint

Scholar 4 hours ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 2 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Appreciated 4 days ago, created a post with more than 5 votes. For C: Detect repeats problematic for PCR
Teacher 6 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 6 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Scholar 7 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 8 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Teacher 8 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 8 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Scholar 9 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Popular Question 10 days ago, created a question with more than 1,000 views. For Tool to identify recurrent mutations directly from VCF
Scholar 13 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 13 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 15 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 15 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Teacher 16 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Popular Question 16 days ago, created a question with more than 1,000 views. For Tool to identify recurrent mutations directly from VCF
Scholar 18 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 20 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 20 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Scholar 21 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Scholar 22 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?

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