phastCons100way.UCSC.hg19 equivalent for mm10 ?

[Just08]

Hi,

I work with mouse genome (mm10) and i don't find any phastCons100way.UCSC.hg19 equivalent for mm10 to do the "Split reads" part of bioconductor tutorial.

Sorry for my bad english.

Thanks in advance for your help.

[jianhong]

You can skip that parameter. It will save you time.

Jianhong.

On Fri, Jul 10, 2020 at 12:21 PM Just08 [email protected] wrote:

Hi,

I work with mouse genome (mm10) and i don't find any phastCons100way.UCSC.hg19 equivalent for mm10 to do the "Split reads" part of bioconductor tutorial.

Sorry for my bad english.

Thanks in advance for your help.

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-- Yours sincerely, Jianhong Ou

[Just08]

Thank you for your answer . When I launch splitBam it output me only the shifted bam with the index but not the bam split by length.

Here a part of the errors log : ` [bam_translate] PG tag "MarkDuplicates" on read "NB500967:20:HNJHTBGXB:2:23202:22212:9651" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. [bam_translate] PG tag "MarkDuplicates" on read "NB500967:20:HNJHTBGXB:1:11105:8407:8325" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [W::bgzf_read_block] EOF marker is absent. The input is probably truncated

` The bam I use is the ouptut of picard MarkDuplicates with the REMOVE_DUPLICATE=true options and there is no errors in summary of picard ValidateSamFile.

Justine

[jianhong]

Hi,

Try to remove the PG label from your tags.

Jianhong.

On Thu, Jul 16, 2020 at 8:24 AM Just08 [email protected] wrote:

Thank you for your answer . When I launch splitBam it output me only the shifted bam with the index but not the bam split by length.

Here a part of the errors log : [bam_translate] PG tag "MarkDuplicates" on read "NB500967:20:HNJHTBGXB:2:23202:22212:9651" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. [bam_translate] PG tag "MarkDuplicates" on read "NB500967:20:HNJHTBGXB:1:11105:8407:8325" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID. [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [W::bgzf_read_block] EOF marker is absent. The input is probably truncated The bam I use is the ouptut of picard MarkDuplicates with the REMOVE_DUPLICATE=true options and there is no errors in summary of picard ValidateSamFile.

Justine

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[Just08]

Thanks you, it remove PG error but not :

[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [W::bgzf_read_block] EOF marker is absent. The input is probably truncated

The only way splitBam function work for me is when I launch it by chromosome and then do corresponding merge (probably a memory problem but I have 48 Go of RAM on my workstation). But now , how to reproduce the objs variable of the tutorial ?

Justine

[jianhong]

Could you share me the bam file and script you are using?

Best!

Your sincerely,

Jianhong Ou

On Jul 21, 2020, at 6:07 AM, Just08 [email protected] wrote:

 Thanks you, it remove PG error but not :

[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes [W::bgzf_read_block] EOF marker is absent. The input is probably truncated

The only way splitBam function work for me is when I launch it by chromosome and then do corresponding merge (probably a memory problem but I have 48 Go of RAM on my workstation). But now , how to reproduce the objs variable of the tutorial ?

Justine

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[Just08]

I think I can't but could you tell me if the following code can be the solution to create the objs variable ? It works but I just want to know if there is no problem to do that .

Thanks

bamfiles <- paste(paste(wd,paste(outPath,bamfile.labels,sep = "\\"),sep=""),
                     c("NucleosomeFree.sorted.bam",
                     "mononucleosome.sorted.bam",
                     "dinucleosome.sorted.bam",
                     "trinucleosome.sorted.bam"),sep = "\\")


indexBam(bamfiles,overwrite=FALSE)


nf <-readBamFile( bamfiles %>% 
   str_subset(pattern = "NucleosomeFree"))
  

mono <- readBamFile( bamfiles %>% 
   str_subset(pattern = "mononucleosome"))


di <- readBamFile( bamfiles %>% 
   str_subset(pattern = "dinucleosome"))


tri <- readBamFile( bamfiles %>% 
   str_subset(pattern = "trinucleosome"))

objs <- GAlignmentsList(NucleosomeFree=nf, mononucleosome=mono,dinucleosome=di,trinucleosome=tri)

[fuyudawn]

I solved this error by updating my R from 3.6.3 to 4.1.2 and reinstalling all packages.