Issue in unite funtion

[Anjaligarg006]

I am trying the unite large samples after filtering its seem fine, but after unite chromosome and strand column are showing meta character instead of name chr start end strand coverage1 numCs1 numTs1 coverage2 3500000 \037 384725 384725 15 14 1 14
3500001 - 387067 387067 21 13 8 17
3500002 # 389072 389072 18 12 6 11
3500003 \b 391998 391998 22 21 1 27
3500004 + 391999 391999 \b 26 25 1 18
3500005 , 394729 394729 31 19 12 22

[alexg9010]

Hi @Anjaligarg006 ,

Could you please post more details? What code did you run? Are you using in-memory or tabix-based objects? Which version of methylKit are you using?

Best, Alex

[Anjaligarg006]

Hi,this is. my code ` methobj=methRead(file_list, sample.id=as.list(sample_ids), assembly="canFam4", treatment=treatment_id, context="CpG", dbdir = "methyDB",dbtype="tabix", pipeline = "bismarkCytosineReport")

#########################################

Filtering samples based on read coverage

filtered.methobj=filterByCoverage(methobj,lo.count=10,lo.perc=NULL, hi.count=NULL,hi.perc=99.9)

merging samples

meth=methylKit::unite(filtered.methobj, destrand=FALSE) ` I am using tabix-based object and 1.30.0 version of methylkit.

[alexg9010]

The code looks fine to me, but the chromosome names seem off in the output you showed. Could you please send a tiny subset of your data that recreates the issue.

Best would be a few hundred lines from the bismark cytosine reports, please make sure to include enough lines with CpG context.

[Anjaligarg006]

Hi, When I am trying with two samples it is working fine. But when including more samples it shows meta characters in chromosome name column. Can you please help me with this?

[alexg9010]

Hi @Anjaligarg006,

Can you share some of the files that reproduce the issue?

Best, Alex

[Anjaligarg006]

@alexg9010 can you please share some email id so that I can share with you?

[alexg9010]

Please share it with alex dot gos90 at gmail dot com .

Best, Alex