Bedtools intersect QTL animalgenome

Question

[Wietje]

I am trying to find QTLs in the bovine genome (downloaded as bed-file from the CattleQTLdb here: http://www.animalgenome.org/cgi-bin/QTLdb/BT/download?file=bedUMD_3.1) that intersect with candidate lnc's I've filtered out with FEElnc.

I have unzipped the file and tried the bedtools intersect command:

$ bedtools intersect -a QTL-file -b candidate-lnc-file > intersect_qtl_lnc

but I get this Error-message: * ERROR: too many digits/characters for integer conversion in string . Exiting...

Has anyone encountered this problem before? Is there an additional conversion step I need to make? I appreciate your efforts! thx

[James Ashmore]

Could you post a small example of your -a and -b files please?

Answer 1

[Wietje]

It's alright, I found the bug -> removing lines with missing coordinates and duplicates does the trick (http://seqanswers.com/forums/showthread.php?t=69484), it works now.

[microfuge]

Just an observation from the bedtools source

if (len < 1 || len > 10) {
    fprintf(stderr, "***** ERROR: too many digits/characters for integer conversion in string %s. Exiting...\n", str);
    exit(1);

}

The coordinates seem to be under 10 digits. I could get get the error after giving a fake bed file with chromEnd of 10 digits. But the limits seems not relevant for everyday use.

Answer 2

[Wietje]

The QTL-file (bed format) starts with several comment lines, each starting with # and the "normal content" look like this:

X 65152465 65152505 Body weight (mature) QTL (65327) + 65152465 65152505 . . . .

X 65221953 65221993 Body weight (mature) QTL (65328) + 65221953 65221993 . . . .

X 64847299 64847339 Body weight (mature) QTL (65329) + 64847299 64847339 . . . .

I tried reducing the file to the first three columns but that doesn't help either.

The lnc-file (gtf format) has the following structure:

17 StringTie exon 66683795 66684113 1000 - . gene_id "MSTRG.4748"; transcript_id "MSTRG.4748.1"; exon_number "6"; 3 StringTie exon 12569270 12569448 1000 + . gene_id "MSTRG.11128"; transcript_id "MSTRG.11128.16"; exon_number "1"; 3 StringTie exon 12576517 12576543 1000 + . gene_id "MSTRG.11128"; transcript_id "MSTRG.11128.16"; exon_number "2";

I have worked with the lnc-file before, so the problem seems to be with the downloaded file.