Closed rejo27 closed 3 months ago
Hi @rejo27, and thank you for your interest in TOBIAS. Unfortunately, I need more information to help you. For example, I'm unsure what you mean by "single mode". Did you run BINDetect for each time point individually? In general, providing the actual tool calls would help. However, before you do that let me recommend our TOBIAS snakemake pipeline. This pipeline does a full TOBIAS analysis by calling the TOBIAS tools in order so you don't have to worry about calling each of the tools yourself.
Regarding your questions:
bindetect_figures.pdf
).I hope this answers some of your questions. And again I want to recommend our TOBIAS pipeline which may help you to fix some of your questions/issues.
Please let me know how it went. Best wishes, Hendrik
I just came back from a business trip, so I'm sorry for replying to you so late. I didn't explain my problem clearly, I will explain it with a practical example.
for treat in cond_A cond_B cond_C cond_D
do
TOBIAS BINDetect \
--motifs ${motifMeme} \
--signals 02-FootprintScores/${treat}_footprints.bw \
--genome ${genome} \
--peaks ${ConsensusPeak} \
--peak_header 00-sample_ConsensusPeakDir/${treat}/peaks_annotated_header.txt \
--outdir 03-BINDetect/${treat} \
--cond_names ${treat} \
--cores 8 > ./03-BINDetect/BINDetect.${treat}.log 2>&1
done
The following results are output for the two time points (cond_A, cond_B)
$ head AT5G67000_cond_A_bound.bed
chr1 20278 20288 AT5G67000 8.25197 - chr1 19962 23171 1.28774
$ head AT5G67000_cond_B_bound.bed
chr1 20278 20288 AT5G67000 8.25197 - chr1 19962 23171 1.10002
Because 1.28774 > 1.10002, does it mean that in cond_A, the binding ability of AT5G67000 at chr1 20278 20288 is greater than that of cond_B?
$ head AT5G67000_cond_A_bound.bed
chr1 20278 20288 AT5G67000 8.25197 - chr1 19962 23171 1.10002
chr1 21190 21200 AT5G67000 10.5598 - chr1 19962 23171 2.49043
In cond_A, it is predicted that AT5G67000 has two binding sites, chr1:20278-20288 and chr1:21190-21200. Since 2.49043 > 1.10002, does it mean that the binding ability of AT5G67000 at chr1:21190-21200 is greater than that at chr1:20278-20288?
Thanks. Looking forward to your reply.
Thank you this made it very clear!
Thank you so much!
Hi, First of all, thank you for the TOBIAS. This is a powerful tool. I now have multiple time-sequential ATAC-seq data (cond_A, cond_B, cond_C, cond_D). I run the tools in order
ATACorrect -> ScoreBigwig -> BINDetect
with the merge peak (cat *peak.bed > merge.bed
) in single mode. I have the following problems: