too many error

[smm19900210]

[Mon Apr 25 15:18:20 2016] Extending the seeds...........Use of uninitialized value $read_label[3] in substitution (s///) at UROBORUS.pl line 726, line 1. Use of uninitialized value $read_length in numeric lt (<) at UROBORUS.pl line 728, line 1. Use of uninitialized value in numeric lt (<) at UROBORUS.pl line 728, line 1. Use of uninitialized value $read_label[3] in substitution (s///) at UROBORUS.pl line 726, line 2. Use of uninitialized value $read_length in numeric lt (<) at UROBORUS.pl line 728, line 2. Use of uninitialized value in numeric lt (<) at UROBORUS.pl line 728, line 2. Use of uninitialized value $read_label[3] in substitution (s///) at UROBORUS.pl line 726, line 3. Use of uninitialized value $read_length in numeric lt (<) at UROBORUS.pl line 728, line 3. Use of uninitialized value in numeric lt (<) at UROBORUS.pl line 728, line 3. Use of uninitialized value $read_label[3] in substitution (s///) at UROBORUS.pl line 726, line 4. Use of uninitialized value $read_length in numeric lt (<) at UROBORUS.pl line 728, line 4. Use of uninitialized value in numeric lt (<) at UROBORUS.pl line 728, line 4. Use of uninitialized value $read_label[3] in substitution (s///) at UROBORUS.pl line 726, line 5. Use of uninitialized value $read_length in numeric lt (<) at UROBORUS.pl line 728, line 5. how can i deal with it？

[xiaofengsong]

Currently, UROBORUS can only apply on the total RNA-seq with length of 50-100bp. The reason is that the @seq_id in R20_1.fastq, and R20_2.fastq we build is too long, tophat can not deal with it. We will try to modify UROBORUS to be used in the long read (>100bp) in the future.

[smm19900210]

thanks xiaofeng, I have another question, like what you say, UROBORUS can only apply on the total RNA-seq with length of 50-100bp, and bowtie1 is used with length of 50bp below，Is this meant that I can not use tophat2 and bowtie2？

[xiaofengsong]

we trimed 50-100bp to be short 20bp anchors. so bowtie1 and bowtie1 index should be used in UROBORUS.

[smm19900210]

thanks, i use tophat2 and bowtie2 to generate unmapped sam file, and then use your UROBORUS to identify circRNA, the number of circRNA is zero.

[xiaofengsong]

Make sure that total RNA-seq data wirh length of 50-100bp (including PolyA minus and PloyA plus) should be used. Could you send me the description of your RNA-seq data

[xiaofengsong]

For all user: circular RNA does not has PloyA tail, so you can not detect any circRNA in PolyA RNA-seq. Do not try to use PolyA RNA-seq data. You should use PolyA minus or total RNA-seq data to detect circular RNA