Hello,

The last line of the report you sent suggests that the file has format problems. I read through your other email and noticed that a few steps were inserted, perhaps because they were needed. However, the line noted here is not in BED format:


On 10/4/11 12:06 PM, shamsher jagat wrote:
'Strand information can not be recognized in this line:
"chr1\t10093\t10093\t10292\t61PDWAAXX100706:4:82:5766:21319

c1 chrom = chr1
c2 start = 10093
c3 end   = 10093
c4 name  = 10292
c5 score = 61PDWAAXX100706:4:82:5766:21319
c6 strand = no data

A description of BED format can be found at http://usegalaxy.org -> "Get Data -> Upload File" (scroll down to BED) or on most tool forms that uses a BED file, such as "Convert Formats -> BED-to-GFF".

A few guidelines (subject to amendment by UCSC readers!):
1 - start is 0-based
2 - start is always a smaller number than end, as coordinates are reported with respect to the forward strand. Start and stop are never the same value.
3 - score is a value between 0-1000, where 0 means undefined.
4 - strand can be "+", "-", or ".", where the "." means undefined.
5 - BED files have to be at least 3 columns, but can have up to 15. Any column used must have all proceeding columns defined, columns 7-12 are usually considered interdependent by the tools that use that data, as are columns 13-15 (newer spec, for microarray data).
6 - BED files often are BED3-6, BED12 or BED15.
7 - some older tools will not recognize columns 13-15 as being "strict BED" format.

Once the data is sorted out, if you continue to have problems, please send in a bug report from an error dataset and note in the comments that the bug is from you, if the account email address is different. Please be sure to leave all input datasets and the error dataset in the history until we can examine and provide feedback.

Thanks,

Jen
Galaxy team

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
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