I have used the Bedtools command intersectBed to check the overlap between two bed files. A is my INDEL file and B is my Reference file. But it is producing an empty output file. I thought the problem was that the file B is much larger than file A. But I tried changing the file order and it is still not creating any output.
Here is the reference B file (larger):
gff_seqname 0 1395 gene 0 +
gff_seqname 0 1395 exon 0 +
gff_seqname 1397 2498 gene 0 +
gff_seqname 1397 2498 exon 0 +
gff_seqname 2524 3619 gene 0 +
Here is my A file with just 51 INDELS:
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME 174708 174713 -GCCGG:2/6
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME 1078686 1078686 +A:105/112
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME 1229123 1229125 -CT:800/870
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME 1234830 1234830 +AT:134/134
NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME 1234833 1234834 -A:134/134
here is my command:
intersectBed -a SOD_pal_BWA_GMM.PE.sorted.bam.sorted_cleaned_GMM.bam.sorted.hr.bam.raw.bed -b sodalis_galaxy.bed -wa -wb >test13.bed
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chromosome names don't match (brentp was first)
not during conversion but you can use the Text Manipulation tools to Cut the first column and then Add Column as first column with the new chromosome
I have managed to add the new Chromosome column but its coming up as the last column. There is no option to choose a particular column (in my case column 1) you want your new data in. Any other ideas? Here is the new data:
0 4171146 source 0 + NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME
0 1395 gene 0 + NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME
0 1395 CDS 0 + NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME
1397 2498 gene 0 + NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME
1397 2498 CDS 0 + NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME
2524 3619 gene 0 + NC_0077121_SODALIS_GLOSSINIDIUS_STR_MORSITANS_CHROMOSOME
And I was wondering how to add 2-3 different chromosomes in the new column. In my case, I have just one chromosome but if it was two then (chr 1, chr 2)?
Here is my B file with modified column 1, still no result. I was wondering if the column need to be exactly similar between two files to get the overlap as still I can see the difference in Chromosome name in column 1 ?
new file B
NC_007712 0 4171146 source 0 +
NC_007712 0 1395 gene 0 +
NC_007712 0 1395 CDS 0 +
NC_007712 1397 2498 gene 0 +
NC_007712 1397 2498 CDS 0 +
the chromosome names need to match EXACTLY
you also need to stop posting a new question when you already suspect what the answer is - you have to make an honest effort otherwise you are just wasting everyone's time - including yours.
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in bed files, the chromosome is the first column. It looks like your chromosomes don't match so there can never be overlaps.
So, do you think I need to change my reference file where the first column is gffseqname to NC0077121SODALISGLOSSINIDIUSSTRMORSITANS_CHROMOSOME to get the match?