.bam files originated from .bedpe as input

[vidaletal]

First of all, many thanks for developing this amazing tool.

I have been used without problems for single-end reads, however, I 'm receiving the following error when I try to use for .bam files originated from .bedpe files.

The error:

$:~/Desktop/Software/HiChipper/HiCPro_PE_norm_hichipper$ ngs.plot.r -G hg19 -R genebody -C config_ngsplot.txt -O metaplot_HiCHIPxHiCxChIPseq -L 5000
Configuring variables...
Using database:
~/Desktop/Software/ngsplot-develop/database/hg19/hg19.ensembl.genebody.protein_coding.RData
Done
Loading R libraries.....Done
Analyze bam files and calculate coverageopen: No such file or directory
Error in FUN(X[[i]], ...) : failed to open SAM/BAM file
  file: '~/Desktop/Software/HiChipper/HiCPro_PE_norm_hichipper/Hi-C-Input_sorteds_interaction.bam'
Calls: headerIndexBam ... indexBam -> sapply -> sapply -> lapply -> FUN -> .Call
Execution halted
$:~/Desktop/Software/HiChipper/HiCPro_PE_norm_hichipper

this is the file

$:~/Desktop/Software/HiChipper/HiCPro_PE_norm_hichipper$ samtools view Hi-C-Input_sorted_interaction.bam | head
NB500931:198:HGYHWBGX7:4:23404:14256:4594	179	chr1	74395	0	74M	chr12	128326315	0	TTTGGGGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGT	EAEAEEEEEEAEEAEE<EE<AEEEEEEEEEEAEEEEEEEEE<EEEEEEEEEEEEAAEEEEE6EAEEEEAAAAAA	AS:i:-15	XN:i:0	XM:i:3	XO:i:0	XG:i:0	NM:i:3	MD:Z:0G2C1A68	YT:Z:UU	RG:Z:BMG	CT:Z:VI
NB500931:198:HGYHWBGX7:4:11608:25382:13700	131	chr1	247762	32	74M	chr20	8107332	0	GATCACTTGAGACCAGGAGTTCGCAACCAGCCTGGACAACATAGGGAGACTCCATCTCCACACATGCCAAAAAA	A6A6A/EEEEE/EAA/EEEE/EEEEEEE6EEE/EEAE/EEEEEEEEEE/AEAA///E/E/E<AAAEEEE/EAAE	AS:i:0	XS:i:-5	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:74	YT:Z:UU	RG:Z:BMG	CT:Z:VI
NB500931:198:HGYHWBGX7:1:11307:24219:17516	163	chr1	526530	32	75M	chr8	274191	0	AGCGGATGATGGATAAACAGAACGTGGTGTGTATACACAGTGGAATATTCTTCAGCCATACAGAGGAATGACAGC	AAAAAEEEEEEEEAEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEAEAEAEA/EEA/	AS:i:0	XS:i:-5	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:75	YT:Z:UU	RG:Z:BMG	CT:Z:VI
NB500931:198:HGYHWBGX7:1:12204:22942:17653	163	chr1	526530	0	75M	chr8	274191	0	AGCGGATGATGGATAAACAGAACGTGGTGTGTATACACAGTGGAATATTCTTGAGCCCGACAGCGGAATGACAGC	AAA6AEEA66EEE///E/EE//AEAE/E6EEE/E/////AA//6E/E/E//E//<E///E/EAEAE/E/E/EE//	AS:i:-14	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:52C4A0T4A11	YT:Z:UU	RG:Z:BMG	CT:Z:VI
NB500931:198:HGYHWBGX7:1:21212:19707:11556	163	chr1	526530	15	75M	chr8	274191	0	AGCGGATGATGGATAAACAGAACGTGGTGTGTATACACAGTGGAATATTCTTCCGCCATACAGAGGAATGACAGC	A/6AA/AA//AEE/EE/EEAE6/EAEAEE/6EE//E/E//EEEEEAEAAE/EE/A/EEEE/EAEEAE/EEEAE//	AS:i:-3	XS:i:-8	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:53A21	YT:Z:UU	RG:Z:BMG	CT:Z:VI
NB500931:198:HGYHWBGX7:1:22311:6282:13191	99	chr1	526530	31	75M	chr8	274191	0	AGCGGATGATGGATAAACAGAACGTGGTGTGTATACACAGTGGAATATTCTTCAGCCATACAGAGGAATGACAGC	/AAAAEA/EAEAEAEEEEE/EEEEAEAE/EE6EEEAEAEEE</A///<EEEEE<AEEEAAEEEEEEAEE/EE/EE	AS:i:0	XS:i:-4	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:75	YT:Z:UU	RG:Z:BMG	CT:Z:VI

I saw this closed thread #9, but not sure if it applies to my case.

Is there a way to use this type of file as input?

Many thanks,

Raphael

[singhsk2622]

Hi Raphael,
Did you figure out the issue and solution for that? i am also facing same issue. please let me know if you have any suggestion.
best,
sachin