User: le2336

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le233660
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Posts by le2336

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Comment: A: How can I get the normalized counts matrix after doing TMM normalization using e
... See this discussion: https://support.bioconductor.org/p/77193 ...
written 2.3 years ago by le233660
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Answer: A: convert SNP posiotions to VCF file
... If your snp positions are in a bed file, this post may help: [Question: bed to vcf format conversion][1] [1]: https://www.biostars.org/p/196063/ ...
written 2.3 years ago by le233660
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Comment: C: Download custom track from UCSC genome browser to local
... 1. Right click on the track 2. Select Show details for feature... 3. Go to [track name] track controls 4. Click on "Update custom track" 5. If you look in the text box under "Edit configuration", there should be a link right after bigDataurl= that would be the path to your custom track. ...
written 2.3 years ago by le233660
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Answer: A: Selecting relevant binding sites according to MACS data
... If you have biological replicates, you might want to use MACS2 in combination with the [Irreproducible Discovery Rate (IDR)][1] pipeline to identify peaks that are reproducibly detected between your replicates. If you only have a single replicate there is a workaround discussed here, though replicat ...
written 2.3 years ago by le233660
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Answer: A: Recommendations for a good motif-finder, for short K-mers?
... Are you trying to perform a *de novo* or targeted motif search? For the former, [DREME][1] is better suited for short (<8 positions) motif discovery. If you already know what k-mers you want to search for, you might want to perform a targeted motif search with [FIMO][2] to improve your sensitivit ...
written 2.3 years ago by le233660
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Answer: A: Separation of Alleles from a Gene Mapping
... [asSeq][1] could be helpful, specifically steps 5.1 to 5.3 in the vignette [here][2]. [1]: http://www.bios.unc.edu/~weisun/software/asSeq.htm [2]: http://chrome-extension://encfpfilknmenlmjemepncnlbbjlabkc/http://www.bios.unc.edu/~weisun/software/asSeq.pdf ...
written 2.3 years ago by le233660
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Answer: A: Bowtie default number of mismatches
... By default, Bowtie is set to tolerate up to 2 mismatches in the first 28 bases on the left end (the "seed") of the read. http://bowtie-bio.sourceforge.net/manual.shtml#the-bowtie-aligner ...
written 4.0 years ago by le233660
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Comment: C: Fix SAM flags on quality filtered paired-end BAM file
... This is useful to know. Thank you! ...
written 4.0 years ago by le233660
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Comment: C: Fix SAM flags on quality filtered paired-end BAM file
... This works perfectly. Thank you so much! ...
written 4.0 years ago by le233660
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Fix SAM flags on quality filtered paired-end BAM file
... Hello, I have a BAM file of paired-end reads that have been quality filtered. I would like to salvage those reads whose mates have been filtered out and continue using them in my analysis (I would also appreciate any input on whether this is acceptable practice). Since some of my downstream tools g ...
sam flag paired-end read bam file written 4.0 years ago by le233660 • updated 4.0 years ago by James Ashmore2.6k

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Popular Question 3.0 years ago, created a question with more than 1,000 views. For Fix SAM flags on quality filtered paired-end BAM file
Supporter 6.2 years ago, voted at least 25 times.

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