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bug report: junction extract tool should not count overlapping reads as double support for a junction #187

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yfarjoun opened this issue Jun 26, 2024 · 0 comments · May be fixed by #196
Open

bug report: junction extract tool should not count overlapping reads as double support for a junction #187

yfarjoun opened this issue Jun 26, 2024 · 0 comments · May be fixed by #196

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@yfarjoun
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In the current implementation, read-mates can provide 2 "counts" to the same junction if they both span it. This results in inflated counts and therefore inflated significance when downstream tools consider the counts.

I would like to advocate for each queryname to be able to provide a maximum of 1 count towards any single junction. This must be implemented carefully so memory use doesn't spike too much.
TimD1 added a commit to fulcrumgenomics/regtools that referenced this issue Jul 1, 2024
@TimD1
fix: junctions extractor count overlapping read pairs once
4209eb6 
 - closes griffithlab#187, implemented by adding set of `reads` to `Junction`, and
   only incrementing `read_count` if read has not been seen yet
 - this commit should also increase RegTools speed by removing the barcode
   updating bottleneck caused by repeatedly copying the barcode map
TimD1 added a commit to fulcrumgenomics/regtools that referenced this issue Jul 2, 2024
@TimD1
fix: junctions extractor count overlapping read pairs once
13a3e44 
 - closes griffithlab#187, implemented by adding set of `reads` to `Junction`, and
   only incrementing `read_count` if read has not been seen yet
 - this commit should also increase RegTools speed by removing the barcode
   updating bottleneck caused by repeatedly copying the barcode map
TimD1 added a commit to fulcrumgenomics/regtools that referenced this issue Jul 2, 2024
@TimD1
fix: junctions extractor count overlapping read pairs once
19644c1 
 - closes griffithlab#187, implemented by adding set of `reads` to `Junction`, and
   only incrementing `read_count` if read has not been seen yet
 - this commit should also increase RegTools speed by removing the barcode
   updating bottleneck caused by repeatedly copying the barcode map
TimD1 added a commit to fulcrumgenomics/regtools that referenced this issue Jul 2, 2024
@TimD1
fix: junctions extractor count overlapping read pairs once
70fd322 
 - closes griffithlab#187, implemented by adding set of `reads` to `Junction`, and
   only incrementing `read_count` if read has not been seen yet
 - this commit should also increase RegTools speed by removing the barcode
   updating bottleneck caused by repeatedly copying the barcode map
TimD1 added a commit to fulcrumgenomics/regtools that referenced this issue Jul 3, 2024
@TimD1
fix: junctions extractor count overlapping read pairs once
0e7ae9b 
 - closes griffithlab#187, implemented by adding set of `reads` to `Junction`, and
   only incrementing `read_count` if read has not been seen yet
 - this commit should also increase RegTools speed by removing the barcode
   updating bottleneck caused by repeatedly copying the barcode map
 - updated regtools to v1.1.0
TimD1 added a commit to fulcrumgenomics/regtools that referenced this issue Sep 19, 2024
@TimD1
fix: junctions extractor count overlapping read pairs once
9f5e456 
 - closes griffithlab#187, implemented by adding set of `reads` to `Junction`, and
   only incrementing `read_count` if read has not been seen yet
 - this commit should also increase RegTools speed by removing the barcode
   updating bottleneck caused by repeatedly copying the barcode map
 - updated regtools to v1.1.0
@TimD1 TimD1 linked a pull request Sep 19, 2024 that will close this issue
Open
@santataRU santataRU mentioned this issue Oct 20, 2024
Open
@TimD1 TimD1 mentioned this issue Oct 31, 2024
Open
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fix: junctions extractor count overlapping read pairs once fulcrumgenomics/regtools
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@yfarjoun