<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>If you use gff3_merge with the -l flag, then it will check for non-unique ID's and give new IDs to make them unique. Also in general it is better just to use the cufflinks results and exclude tophat results as they tend to be very noisy and decrease the quality of the final models overall.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> hueytyng <<a href="mailto:cynsb1987@gmail.com">cynsb1987@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Sunday, May 4, 2014 at 7:58 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Non-unique top level ID<br></div><div><br></div><div dir="ltr"><div><div><div>Hi Carson,<br></div><div><br></div>I ran MAKER using RNAseq as evidence (tophat+cufflinks). The gff file is provided to Maker under "est_gff". Maker runs fine but there are a few failed contigs, and these error messages in my log:<br><br>ERROR: Non-unique top level ID for 1:JUNC00010801:0<br>While this is technically legal in GFF3, it usually<br>indicates a poorly fomatted GFF3 file (perhaps you<br>tried to merge two GFF3 files without accounting for<br>
unique IDs). MAKER will not handle these correctly.<br><br>--> rank=2, hostname=safs-raijen<br>ERROR: Failed while prepare section files<br>ERROR: Chunk failed at level:12, tier_type:3<br>FAILED CONTIG:scaffold11129|size28423<br><br></div>I do see multiple IDs in my gff. I have 9 RNAseq samples, is the way I merged them causing the error?<br>This is what I've done to prepare the gff:<br></div><br>1. merge cuffmerge output<br><div><div style="margin-left:40px">
cuffmerge -o <outputdir> -p 4 assembly_list.txt<br></div><div style="margin-left:40px">cufflinks2gff3 merged.gtf > merged.gff
</div><div><div><p>2. merge junctions <br></p><p style="margin-left:40px">find -name "junctions.bed" -exec cat {} \; >> all_junctions.bed</p><p style="margin-left:40px">tophat2gff3 all_junctions.bed > all_junctions.gff <br></p>3. combine cuffmerge and junctions<br></div><div><p style="margin-left:40px">gff3_merge -o tophatandcufflinks.gff merged.gff all_junctions.gff <br></p><p>4. provide in opts file<br></p><p style="margin-left:40px">est_gff=tophatandcufflinks.gff #EST evidence from an external gff3 file
</p><div><br></div><div>Thank you<br><br></div><div>Jenny<br></div><div><br><br><div><br></div></div></div></div></div></div>
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