MACS2 and BED file

Question

[qudrat.nii]

I have run bowtie2 and then bam file sorted by name was converted to bed file after removing mitochondrial DNA and random sequences.

When I use blacklisted regions bed file to filter my bed file it shows error.

The error is that many rows in bed file are blank.

[rpolicastro]

You should include the code you ran and the exact error it produced.

[qudrat.nii]

bedtools intersect -a SRR14646436.bed -b wgEncodeDacMapabilityConsensusExcludable.bed -v >x.bed
Error: Invalid record in file aligned_folder/bedfile/SRR14646436.bed. Record is 
.   -1  -1  .   -1  -1  SRR14646436.5   0   .   .

and bedfile look like this below....

## Heading ##cat SRR14646436.bed | head
chr2    19322064    19322214    chr2    19322137    19322287    SRR14646436.1   42  +   -
chr15   93651161    93651311    chr15   93651194    93651344    SRR14646436.2   42  +   -
chr5    3871291 3871441 chr5    3871319 3871469 SRR14646436.3   42  +   -
chr6    139577220   139577370   chr6    139577327   139577477   SRR14646436.4   42  +   -
.   -1  -1  .   -1  -1  SRR14646436.5   0   .   .
chr1    62856800    62856950    chr1    62856803    62856953    SRR14646436.6   42  +   -
.   -1  -1  .   -1  -1  SRR14646436.7   0   .   .
chr15   60337914    60338064    chr15   60337944    60338094    SRR14646436.8   42  +   -
.   -1  -1  .   -1  -1  SRR14646436.9   0   .   .
.   -1  -1  .   -1  -1  SRR14646436.10  0

[rpolicastro]

That bed file looks malformed. There might have been an error when generating or manipulating it earlier in your processing pipeline.