User: rbronste
rbronste • 170
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Posts by rbronste
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... The gencode retrieval you suggest here is very helpful, I inputted a .txt file of 380 common gene names and received back a `gencode.vM18.tss.filtered.bed` that had 359 IDs. Is there a way to easily identify which were not converted and maybe a way to add those as well? Or do you do this manually? ...
written 7 days ago by
rbronste • 170
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... Yes I actually tried this (--delim \t) but comes up looking like the following:
0.000758255664811437t-42960
So its taking the last column in my peak file (FDR) and adding on the distance. Kind of odd. ...
written 8 days ago by
rbronste • 170
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... Very helpful thank you!
Is there a way to set the `--delim` to establish the distance as a separate column? ...
written 8 days ago by
rbronste • 170
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... Basically Id like to take this set of filtered TSSs and use `closest-features` to filter a peak list for those peaks that fall within lets say 1 mb of this TSS list, however adjusting the downstream measure by the length of the gene harboring the TSS. Does that sort of make sense? Basically I guess ...
written 11 days ago by
rbronste • 170
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... One final question on this, I am trying to see if these particular peaks are within a certain distance of the TSSs this code allows me to isolate, lets say 1MB on either side but if I wanted to to adjust in the downstream direction also for the length of the gene is there a way that closest-feature ...
written 11 days ago by
rbronste • 170
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... Yes I am using mm10, this is very helpful thank you! ...
written 11 days ago by
rbronste • 170
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... If I have a list of common gene names such as the following:
Kcnip1
Nat9
Zfp523
Akap1
Kif19a
St18
Mettl1
Uba7
Pde3b
Gstm7
H13
Slc20a1
Lrig2
Elovl2
Zfp185
Trmt112
Egfr
Klhdc1
Cand2
Macrod1
Kcns1
Slc35a5
Anp32 ...
written 12 days ago by
rbronste • 170
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... Yes its helpful but I was looking for best conversion method of common gene names to RefSeq or UCSC etc outside of Table Browser which appears to be lacking in this respect. ...
written 12 days ago by
rbronste • 170
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... Just trying for simplest way to take a set of common gene names and generate a bed interval file of +/- 2kb of each gene TSS? Thanks. ...
written 12 days ago by
rbronste • 170
• updated
11 days ago by
Alex Reynolds ♦ 25k
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Comment:
C: Closest gene to set of intervals
... One other quick question, how can I maintain a header through sort-bed and closest-features - as it gives me an error indicating my first line in closest-features is not a chromosome start even when I have the --header flag on. Thanks! ...
written 12 days ago by
rbronste • 170
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