User: christylynn002
christylynn002 • 0
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Posts by christylynn002
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... 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 ...
written 2.8 years ago by
christylynn002 • 0
• updated
12 weeks ago by
RamRS ♦ 19k
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... CS means splicing mutation. I am unsure about the other ones
...
written 2.9 years ago by
christylynn002 • 0
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Comment:
C: bedtools intersect without range
... Perfect. Thank you.
...
written 3.3 years ago by
christylynn002 • 0
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... 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 ...
written 3.3 years ago by
christylynn002 • 0
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... I have answered my own question. Could this be removed?
...
written 3.4 years ago by
christylynn002 • 0
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... 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 ...
written 3.5 years ago by
christylynn002 • 0
• updated
10 months ago by
Biostar ♦♦ 20
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... Perfect. Thank you!
...
written 3.5 years ago by
christylynn002 • 0
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... Does this give you every individual exon for the region? Are they only coding exons?
...
written 3.5 years ago by
christylynn002 • 0
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... 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
christylynn002 • 0
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... 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 ...
written 3.5 years ago by
christylynn002 • 0
• updated
3.5 years ago by
Jorge Amigo ♦ 11k
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