phastCons100way.UCSC.hg19 equivalent for mm10 ?

Question

phastCons100way.UCSC.hg19 equivalent for mm10 ?

Just08 opened this issue 4 years ago · comments

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 OU · Answer 1 · Sat Jul 11 2020 00:33:04 GMT+0800 (China Standard Time)

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

…

On Fri, Jul 10, 2020 at 12:21 PM Just08 ***@***.***> 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. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#28>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLBEA73QR7VZWRUD4TTKTDR245ZJANCNFSM4OWXTG6Q> .

-- Yours sincerely, Jianhong Ou

Just · Answer 2 · Thu Jul 16 2020 20:24:03 GMT+0800 (China Standard Time)

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 OU · Answer 3 · Thu Jul 16 2020 20:41:45 GMT+0800 (China Standard Time)

Hi, Try to remove the PG label from your tags. Jianhong.

…

On Thu, Jul 16, 2020 at 8:24 AM Just08 ***@***.***> 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 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABLBEA32HNH5EW6CSEEODGTR33WPHANCNFSM4OWXTG6Q> .

-- Yours sincerely, Jianhong Ou

Just · Answer 4 · Tue Jul 21 2020 18:06:59 GMT+0800 (China Standard Time)

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 OU · Answer 5 · Tue Jul 21 2020 18:45:27 GMT+0800 (China Standard Time)

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 ***@***.***> 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 — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

Just · Answer 6 · Tue Jul 21 2020 18:54:49 GMT+0800 (China Standard Time)

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)

lj^2 · Answer 7 · Thu Nov 03 2022 17:38:28 GMT+0800 (China Standard Time)

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