User: Eric Lim

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Eric Lim1.2k
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Posts by Eric Lim

<prev • 144 results • page 1 of 15 • next >
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Answer: A: MaxEntScan score interpretation
... You need to ask more specific questions for us to provide better answers. In the nutshell, it's scoring a 9-mer (for 5' splice site) and a 23-mer (for 3' splice site) against the consensus (representative) sequence built from all the splice sites in the given species. For 5' splice site (ss), 3 exo ...
written 18 days ago by Eric Lim1.2k
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Comment: C: samtools covert to bam, sort and index all gz.sam
... From personal experience, `sambamba` runs faster. After I made the switch, I haven't gone back to benchmark `samtools` with the latest versions in the past couple of years, so the 2 tools might perform similarly now. Instead of ramping up all the available cores to run jobs simultaneously, providing ...
written 5 weeks ago by Eric Lim1.2k
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Comment: C: How to write all the possible translation into a new fasta file?
... Nice! I knew there must be a way to translate 6-way within the module. ...
written 6 weeks ago by Eric Lim1.2k
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Answer: A: How to write all the possible translation into a new fasta file?
... Assuming [/scratch/tmp/biostars/biopython_translate_allframes]$ cat test.fa >a agctagctagc >b gctagctgctag >c gatcgatcgatcga >d gctgctagctagct >e gctagctagctag Something along this should work fine. with open('test.translated.fa', 'w ...
written 6 weeks ago by Eric Lim1.2k
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Comment: C: How to write all the possible translation into a new fasta file?
... It'd be helpful to post some code snippets to illustrate what you'd tried. Without checking into biopython's ability to translate 3 frames directly from the interface, one approach can be `rec.seq.translate()`, `rec.seq[1:].translate()`, and `rec.seq[2:].translate()`. ...
written 6 weeks ago by Eric Lim1.2k
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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 9 weeks 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 3 months 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 3 months 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 3 months 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 3 months ago by Eric Lim1.2k

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Scholar 7 months ago, created an answer that has been accepted. For A: Two multifasta files with the same sequences, but different headers. How to chan
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Scholar 2.3 years ago, created an answer that has been accepted. For A: Two multifasta files with the same sequences, but different headers. How to chan

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