User: Eric Lim

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Eric Lim1.2k
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2 years, 12 months ago
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Posts by Eric Lim

<prev • 139 results • page 1 of 14 • next >
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Comment: C: How to recreate FASTQ from BAM
... I rarely use STAR-Fusion, but I'd assume the reconstructed fastqs are missing unmapped reads from the normal alignment, which contain reads that are used to build chimeric and circular alignments. You might need to use `--outSAMunmapped Within`. ...
written 2 days ago by Eric Lim1.2k
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Comment: C: Detecting antisense RNA in unstranded RNA-Seq data
... De novo discovery of antisense transcripts using unstranded sequencing data can be challenging. One trivial approach is to construct a list of annotated antisense transcripts whose splice sites do not overlap with the corresponding sense transcripts that code for proteins. You can use reads that are ...
written 4 weeks ago by Eric Lim1.2k
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Comment: C: eCLIP peak calling
... We have had success with the CTK toolkits across various CLIP data. Installation can be a bit painful but I think it's worth the investment. https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation ...
written 6 weeks ago by Eric Lim1.2k
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Comment: C: -bash: ./HeatMap.R: cannot execute binary file. Why is this?
... Of course. Now everybody knows I hardly run any R script. :D ...
written 7 weeks ago by Eric Lim1.2k
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Comment: C: need code for sorting fasta header
... Assuming the (mitochondrion) is always there, this is what I can think on the of my head `cut -f1 -d'(' header.txt | sort`. There will be an empty space at the end and can be removed by `sed 's/ *$//'`. ...
written 7 weeks ago by Eric Lim1.2k
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Comment: C: -bash: ./HeatMap.R: cannot execute binary file. Why is this?
... What does it return with the command `file HeatMap.R`? ...
written 7 weeks ago by Eric Lim1.2k
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Comment: C: -bash: ./HeatMap.R: cannot execute binary file. Why is this?
... Why is your R script binary? Have you tried `Rscripts myscripts.R`? The `cannot execute binary file` typically has something with incompatible architectures. ...
written 7 weeks ago by Eric Lim1.2k
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Comment: C: 5', 3' SS and Intron retention read count using STAR out.tab
... Yes, my best understanding is that most tools rely on annotated exons to call intron retention (IR). Some tools infer IR by accessing exon-intron junction reads at both 5'ss and 3'ss. This approach is generally correct but will produce some false positives on those introns when both splice sites are ...
written 7 weeks ago by Eric Lim1.2k
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Comment: C: Conda on MacOS
... I think the OP might have been mistaken with `wget -O`. His original post, wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh bash Miniconda3-latest-MacOSX-x86_64.sh should have been sufficient to install miniconda. I'm not sure where the curl's error came about. ...
written 7 weeks ago by Eric Lim1.2k
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Comment: C: 5', 3' ASS and Intron retention read count using STAR out.tab
... You might be interested in tools like SGSeq: https://bioconductor.org/packages/release/bioc/html/SGSeq.html It reads from the aligned bam. It isn't the fastest tool, but from personal experience, it's pretty sensitive for both annotated and novel events. Note: 3'ss and 5'ss stand for 3' splice sit ...
written 7 weeks ago by Eric Lim1.2k

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Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Difference between GTF file with CHR and without CHR. ENSEMBL
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