Update CUT&RUN tutorial #5104
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Update CUT&RUN tutorial #5104
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lldelisle
commented
Jun 29, 2024
| > > 1. ~55% and ~57% | ||
| > > 2. 100% | ||
| > > 1. ~55% for Read 1 and ~57% for Read 2 | ||
| > > 2. The last line indicates that 3.5% of pairs have been removed. |
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@heylf could you confirm it makes sense (the output of bowtie2 does not have 300k reads as input).
| > This is what we call dovetailing and we want to consider this pair as a valid concordant alignment. | ||
| {: .comment} | ||
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I decided to remove this part because the tutorial is using TrimGalore and removes adapters even if they are a single base pair.
| @@ -264,7 +245,7 @@ repetitive regions but keep reads falling into regions present in alternate loci | |||
| > | |||
| > > <solution-title></solution-title> | |||
| > > | |||
| > > 41.46+57.51=98.97% | |||
| > > 36.47+62.39=98.86% | |||
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I don't know why these number changed (maybe the version of bowtie2)...
| > > > 2. 454 peaks | ||
| > > > 3. Our precision is ~ 84%. A high precision is an indicator that we can predict true binding regions with high confidence. | ||
| > > > 1. 2,865 peaks (this is the number of lines of our last output) | ||
| > > > 2. About 4000 peaks (Rep1 and Rep2 has about 6-7 thousand peaks each) |
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@heylf Here I am not sure of what you consider false positive but I guess they are peaks in a single replicate which are not overlapping the second replicate.
| @@ -622,7 +603,7 @@ Let's find out the sequence motifs of the TF GATA1. Studies have revealed that G | |||
| > > | |||
| > > > <solution-title></solution-title> | |||
| > > > | |||
| > > > 1. !!!! Where is this info? !!! | |||
| > > > 1. Where is this info? | |||
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Could not find this info
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xref #5164 |
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Try to make the CUT&RUN tutorial out.
I ran the tutorial on usegalaxy.eu.