User: christylynn002

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Posts by christylynn002

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Genes on negative strand?
... I'm getting a little bit confused about how/why the UCSC reports genes on the negative strand. I've noticed that while downloading gene sequences, I need to use the reverse complement of some of the sequences to get the correct ordering of exons with the correct splice sites denoted. This doesn't ma ...
gene sequence written 2.8 years ago by christylynn0020 • updated 12 weeks ago by RamRS19k
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Answer: A: HGMD mutation naming convention
... CS means splicing mutation. I am unsure about the other ones ...
written 2.9 years ago by christylynn0020
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Comment: C: bedtools intersect without range
... Perfect. Thank you. ...
written 3.3 years ago by christylynn0020
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bedtools intersect without range
... I have two files: FileA.bed ZC3H14 1 VRK1 2 G6PC 79 tp63dn 3 G6PD 174 FileB.bed ZC3H14 1 VRK1 1 G6PC 14 G6PD 1 tp63dn 2   I would like to intersect the two files with bedtools intersect -a FileA.bed -b FileB.bed -loj however, I do not have a range to intersect t ...
bedtools intersect written 3.3 years ago by christylynn0020
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Comment: C: Obtaining information from UCSC genome table browser
... I have answered my own question. Could this be removed?   ...
written 3.4 years ago by christylynn0020
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Relative Positions +/- strand
... Lets say I have a file that contains all the exon starts and stops of a particular gene that also includes the identification of the strand (+ or -). I have a second file that contains a particular position within that gene that also contains a strand identifier. If I just want to compare the two fi ...
sequence written 3.5 years ago by christylynn0020 • updated 10 months ago by Biostar ♦♦ 20
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Comment: C: Obtaining only coding exons from UCSC table browser
... Perfect. Thank you! ...
written 3.5 years ago by christylynn0020
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Comment: C: Obtaining only coding exons from UCSC table browser
... Does this give you every individual exon for the region? Are they only coding exons? ...
written 3.5 years ago by christylynn0020
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Comment: C: Obtaining only coding exons from UCSC table browser
... I've been able to switch the first and last values like you proposed, but the problem is that the cdsStart and cdsEnd is not necessarily in the first or last exons.  haha. Not for an interview. Just an intermediate step for further analysis  ...
written 3.5 years ago by christylynn0020
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Obtaining only coding exons from UCSC table browser
... Hi all. I'm having trouble producing a file that contains only the coding exons that do not contain UTR's. I've obtained a file from UCSC table browser that looks something like this: #name cdsStart cdsEnd exonCount exonStarts exonEnds NM_017436 43088895 43089957 3 43088 ...
python written 3.5 years ago by christylynn0020 • updated 3.5 years ago by Jorge Amigo11k

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