Question: Join genomic interval
0
scholtz • 60 wrote:
Hi Galaxy team -
We are trying to use the Join (genomic intervals) function on Galaxy Main, but our data files are not recognized as interval files.
dataset 1 (first three lines):
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| chr1 | 14672 | 14673 | chr1 | 14673 | 14673 | G | C | ncRNA_exonic | WASH7P | NA | NA | -1 | -1 | -1 | rs11582131 | NA |
| chr1 | 14762 | 14763 | chr1 | 14763 | 14763 | G | T | ncRNA_exonic | WASH7P | NA | NA | -1 | 0.02 | -1 | NA | NA |
| chr1 | 14791 | 14792 | chr1 | 14792 | 14792 | G | A | ncRNA_exonic | WASH7P |
Dataset 2:
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| locus tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status | |||||||||||||||
| chr1 | 34610 | 36081 | uc001aak.3 | - | - | uc001aak.3 | - | - | chr1:34610-36081 | - | - | 0 | 0 | 0 | OK |
| chr1 | 69090 | 70008 | uc001aal.1 | - | - | uc001aal.1 | - | - | chr1:69090-70008 | - | - | 0 | 0 | 0 | OK |
| chr1 | 321145 | 321207 | uc001aar.2 | - | - | uc001aar.2 | - | - | chr1:321145-321207 | - | - | 0 | 0 | 0 | OK |
We were following the J Goecks Variant analysis workflow for RNSseq, but got stuck at this step.
Any ideas what the problem might be?
Thank you very much,
Beata Scholtz
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modified 3.2 years ago
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Jennifer Hillman Jackson ♦ 25k
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3.2 years ago by
scholtz • 60
