I already have .fa file in Bowtie2Index directory and it's not empty:
These are files with reference gnome:
genome.1.bt2 genome.2.bt2 genome.4.bt2 genome.fa.fai genome.rev.2.bt2 reads_2.fq
genome.3.bt2 genome.fa genome.rev.1.bt2 reads_1.fq
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Have you checked if the created reference fasta file wasn't empty? Mayby you could try to recreate the reference file upon analysis using bowtie2-inspect?
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I tried with all the possible data but am getting the same error about junction. Is it because of the reference genome?
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It seems that you only have 2 reads in your dataset (2 kept reads). I would try a bigger set of reads to start with.
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Tophat2 returns empty junction file: Warning: junction database is empty!
I am using Tophat2 V2.0.7 with this command:
Code:tophat2 -p 1 --library-type fr-unstranded --segment-length 12 /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome Galaxy164-\[FASTQ_Groomer_on_data_152\].fastqsanger
Code:[2013-02-14 03:31:11] Beginning TopHat run (v2.0.7) ----------------------------------------------- [2013-02-14 03:31:11] Checking for Bowtie Bowtie version: 2.0.6.0 [2013-02-14 03:31:11] Checking for Samtools Samtools version: 0.1.18.0 [2013-02-14 03:31:11] Checking for Bowtie index files [2013-02-14 03:31:11] Checking for reference FASTA file Warning: Could not find FASTA file /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa [2013-02-14 03:31:11] Reconstituting reference FASTA file from Bowtie index Executing: /usr/bin/bowtie2-inspect /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome > ./tophat_out/tmp/genome.fa [2013-02-14 03:33:21] Generating SAM header for /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome format: fastq quality scale: phred33 (default) [2013-02-14 03:33:54] Preparing reads left reads: min. length=36, max. length=36, 2 kept reads (0 discarded) [2013-02-14 03:33:54] Mapping left_kept_reads to genome genome with Bowtie2 [2013-02-14 03:34:26] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/3) [2013-02-14 03:34:59] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/3) [2013-02-14 03:35:32] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/3) [2013-02-14 03:36:05] Searching for junctions via segment mapping Warning: junction database is empty! [2013-02-14 03:37:27] Reporting output tracks ----------------------------------------------- [2013-02-14 03:38:48] Run complete: 00:07:37 elapsed
Code:track name=junctions description="TopHat junctions"
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