I ran TopHat and the run was successful but I am unable to figure out why my junction.bed file is empty? can anybody guide?
thanx
thanx
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Last edited by bharati; 06-05-2012, 03:54 AM. -
You'll need to provide a lot more information if you want an answer to that question. -
more information ?? like what?Comment
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can u pls elaborateComment
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Organism and platform used for sequencing. Did the Tophat run produce any errors? Do you have split reads in your alignment?Comment
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actually i used the given command:
/home/tophat-2.0.0.Linux_x86_64/tophat -r -34 --mate-std-dev 36 /home/bowtie2-2.0.0-beta5/example/hg19/hg19 /data1/bowtie_aln/R1_RB002_zip_cat_trim_4_90_Q30_80_matched.fastq /data1/bowtie_aln/R2_RB002_zip_cat_trim_4_90_Q30_80_matched.fastqComment
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do I need to specify some more options along with the above command? Did I missed some thing?Comment
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