Intersectbed Tool Generating Empty File

Question

[bioinfo]

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

[brentp]

in bed files, the chromosome is the first column. It looks like your chromosomes don't match so there can never be overlaps.

[bioinfo]

So, do you think I need to change my reference file where the first column is gffseqname to NC0077121SODALISGLOSSINIDIUSSTRMORSITANS_CHROMOSOME to get the match?

Answer 1

[Istvan Albert]

chromosome names don't match (brentp was first)

[bioinfo]

I used the galaxy (gff to BED) and the refseq (genebank to gff) link you mentioned last time. It automatically created the reference output file in bed format.

[bioinfo]

Is there any option to change the column name for my reference in galaxy during converting gff to BED format?

[Istvan Albert]

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

[bioinfo]

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)?

[bioinfo]

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   +

[Istvan Albert]

the chromosome names need to match EXACTLY

[Istvan Albert]

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.