find_circ

find_circ copied to clipboard

What's the maximum Number of scaffolds (".fa" files) for the find_circ.py "-G" option

7

Hello, Marvin Jens, I'm using your software for plant circRNA identification, however, the "-G (--genome)" option doesn't work with the Error 24 "too many open files", because of the draft...

tw7649116

My dear professor: this process is 10min bowtie2 -p 20 --reorder --mm --score-min=C,-15,0 -q -x /ref/boetiew2_index_rice -U anchors.fq.gz -S bowtieresult.sam this process need 2hours: bowtie2 -p 20 --reorder --mm --score-min=C,-15,0...

songrunxian

Enquiry on --stranded and --standpref argument usage in find_circ!

2

Dear Marvin Jens, Good day! I am currently using the find_circ program developed by you for my work. I noticed there are additional arguments (--stranded & --strandpref). May I know...

cheehowteo

find_circ.py show error

1

bowtie2 -q -U unmapped.fastq -x /Drive1/find_circ/index/bow2_homo --reorder --mm --very-sensitive --score-min=C,-15,0 | /home/aclab/apps/find_circ/find_circ.py -G /home/aclab/homo.fa -p homo --stats homo_sites.log --reads homo.fa >homo.bed [E::sam_parse1] query name too long [W::sam_read1] Parse error at...

aman21392

When running `make` in `test_data` to check the installation of `find_circ` I did, I ran into this: ``` >>> building bowtie2 index bowtie2-build CDR1as_locus.fa bt2_cdr1as_locus > bt2_build.log 2>&1; >>> aligning...

boegel

Option flank is never used in merge_bed.py

2

I was wondering that the fuzzy search in merge_bed.py gives me the same results as without the fuzzy search. I looked into merge_bed.py and saw that this option is never...

ghost