diffbind analyze for wheat
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zgyu12 • 0
@584cc641
Last seen 10 months ago
China
[E::hts_idx_push] Region 536872557..536872641 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6
Error: Error processing one or more read files. Check warnings().
In addition: Warning messages:
1: In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) :
  all scheduled cores encountered errors in user code
2:   file: bam/JW_1.uniq.sort.rmdup.1A.bam 



# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

dbObj <- dba(sampleSheet=samples)
dbObj <- dba.count(dbObj, bUseSummarizeOverlaps=TRUE)

I use the hg38 genome for diffbind is OK, while wheat genome is so big, how can use diffbind to analyze the wheat project?

DiffBind • 726 views
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@james-w-macdonald-5106
Last seen 49 minutes ago
United States

That error doesn't come from DiffBind, but instead it comes from samtools/htslib.

You may be able to index your files using a csi index, but I am not sure that it will then work with DiffBind, as IIRC Rsamtools requires a bai index.

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Thanks, I use cis index for bam, but it raise the same error. May be Rsamtools not support csi index.

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Hi, did you ever solve this issue? I have the same issue using axolotl attic-seq data. Curious to know if there's a solution for diff peak analyses using csi indexing.

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