Hi I am doing a Chip-seq analysis. How do you cut for base sequence content in the final part where some bases tend to go down and some bases up ??? on the galaxy platform. Is it necessary to continue the analysis?
You should do a quality and adapter trimming here, that will probably fix what you see there
the help states:
The current trimming steps are:
ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.
SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold.
LEADING: Cut bases off the start of a read, if below a threshold quality
TRAILING: Cut bases off the end of a read, if below a threshold quality
CROP: Cut the read to a specified length
HEADCROP: Cut the specified number of bases from the start of the read
MINLEN: Drop the read if it is below a specified length
TOPHRED33: Convert quality scores to Phred-33
TOPHRED64: Convert quality scores to Phred-64
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version 2.3.6
I don't think you need to worry about that. Aligner should be able to soft-clip anything that does not map on that end. Carry on with the analysis.
Thanks , but I need to do an exam and I want to cut the final part but i don't understand how can I do that :( with galaxy.my professor said to use the tool " trimmomatic a flexible read trimming tool for illumina ngs data" , but i don't know what i should select among the options to correct only this part . do you know how to do it?,
If you need galaxy specific answers then it is better to post your queries on their help site: https://help.galaxyproject.org/
On galaxy, you will need to use
Insert trimmomatic operationoption and then add the parameterCROP: Cut the read to a specified lengthto keep a certain number of bases (i.e.length - bp you want to remove).https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
Try trim_galore