augustboyle
commented
1 year ago Hello,
I processed the paired end ENCODE data in two steps.
The paired end rule for making BAMs is on the Figshare: https://figshare.com/articles/dataset/Skipper_RNA-protein_interaction_profiles/21206009?file=37612190
Then, I started the GitHub pipeline from BAM input.
On starting from BAM input: 1) Edit the rule all so that the fastq specific output is not requested and it can generate all the needed output from BAMs. 2) Ensure that the informative read parameter is set appropriately, 1 if the crosslink site in in read 1 and 2 if the crosslink site is in read 2.
Another option is to simply use the informative read in the single end pipeline, which we have done when pooling samples on paired end sequencing runs. Because the Yeo lab library design is single end, we don’t make use of any of the read pairing information. In fact most of the reads are trimmed and it does not have any advantage at all. But if you have some larger fragments it could help with the alignment.
Best, Evan
On Oct 4, 2023, at 12:35 PM, Ibrahim Vazirabad @.***> wrote:
Hello,
I would like direction on how to incorporate paired-end eCLIP into the Skipper manifest. The example manifest indicates single-end sequencing with one or two lanes used. How do I add R1 and R2 to a single cell?
-Ibrahim Vazirabad
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FionaMoon
Hello,
I would like direction on how to incorporate paired-end eCLIP into the Skipper manifest. The example manifest indicates single-end sequencing with one or two lanes used. How do I add R1 and R2 to a single cell?
-Ibrahim Vazirabad