Split merged Bam file without replacement

Question

[g.persic1991]

Hi guys,

I have 5 bam (ChIPseq PE data sorted by position) files that came from 5 different murine cortexes (mice that belong to the same group, so biological replicates), however I have a lot of group variability. I'm thinking to merge all this 5 bam (I know that is a dirty things) in order to make a unique bam file (already done using samtools merge) and then split (in a random way) in 5 new bam files... I'll use they to make a Differential analysis with DiffBind

However I don't find a way to split it.

I have try with following command (that allow to split just in 2 bam files...that for now could be a good starting point)

samtools view -H test.bam > f1.sam
cp f1.sam f2.sam
samtools view test.bam | awk '{if(NR%4<2){print >> "f1.sam"} else {print >> "f2.sam"}}'

but seem that the new bam files has some problem because when I try to count the reads in each bam file using

samtools view -c f1.sam > reads.txt 

I obtain the following error

[E::sam_parse1] no SQ lines present in the headerls view -c f2.sam  > reads.txt 
[main_samview] truncated file.

Please, can someone help me?

[Pierre Lindenbaum]

I don't really understand what's your aim. Nevertheless what is the output of :

samtools view -H test.bam | grep SQ

[g.persic1991]

Below the output

@SQ SN:chr1 LN:195471971
@SQ SN:chr2 LN:182113224
@SQ SN:chr3 LN:160039680
@SQ SN:chr4 LN:156508116
@SQ SN:chr5 LN:151834684
@SQ SN:chr6 LN:149736546
@SQ SN:chr7 LN:145441459
@SQ SN:chr8 LN:129401213
@SQ SN:chr9 LN:124595110
@SQ SN:chr10    LN:130694993
@SQ SN:chr11    LN:122082543
@SQ SN:chr12    LN:120129022
@SQ SN:chr13    LN:120421639
@SQ SN:chr14    LN:124902244
@SQ SN:chr15    LN:104043685
@SQ SN:chr16    LN:98207768
@SQ SN:chr17    LN:94987271
@SQ SN:chr18    LN:90702639
@SQ SN:chr19    LN:61431566
@SQ SN:chrX LN:171031299
@SQ SN:chrY LN:91744698
@SQ SN:chrM LN:16299