I am having some trouble with Tophat2/Bowtie2.
I ran the following:
Everything seems to run well:
Except the only output files I get at the end are: deletions.bed, insertions.bed, junctions.bed, log folder, prep_reads.info, and unmapped.bam.
I previously ran the same FASTQ/GTF with Tophat/Bowtie and had millions of mapped reads. Now I'm 0-for-2 with Tophat2.
Does anyone have any suggestions that might help recover an accepted_hits.bam file (other than going back to Tophat/Bowtie)?
I ran the following:
Code:
tophat2 -p 4 -o ~/B73B2 -i 60 -I 4000 -G ~/gDNA.gtf ~/bowtie2_files/MaizeGDNA_B ~/B73B2.fastq
Code:
[2012-10-30 22:17:48] Beginning TopHat run (v2.0.4) ----------------------------------------------- [2012-10-30 22:17:48] Checking for Bowtie Bowtie version: 2.0.0.7 [2012-10-30 22:17:48] Checking for Samtools Samtools version: 0.1.18.0 [2012-10-30 22:17:48] Checking for Bowtie index files [2012-10-30 22:17:48] Checking for reference FASTA file [2012-10-30 22:17:48] Generating SAM header for /home/rdouglas/data/bowtie_files/MaizeGDNA_B format: fastq quality scale: phred33 (default) [2012-10-30 22:18:12] Reading known junctions from GTF file [2012-10-30 22:18:19] Preparing reads left reads: min. length=100, max. length=100, 64796485 kept reads (110651 discarded) [2012-10-30 22:42:11] Creating transcriptome data files.. [2012-10-30 22:42:53] Building Bowtie index from MaizeGDNA_B.fa [2012-10-30 22:52:35] Mapping left_kept_reads to transcriptome MaizeGDNA_B with Bowtie2 [2012-10-30 23:35:53] Resuming TopHat pipeline with unmapped reads [2012-10-30 23:35:53] Mapping left_kept_reads.m2g_um to genome MaizeGDNA_B with Bowtie2 [2012-10-31 09:48:42] Mapping left_kept_reads.m2g_um_seg1 to genome MaizeGDNA_B with Bowtie2 (1/4) [2012-10-31 11:30:34] Mapping left_kept_reads.m2g_um_seg2 to genome MaizeGDNA_B with Bowtie2 (2/4) [2012-10-31 13:12:53] Mapping left_kept_reads.m2g_um_seg3 to genome MaizeGDNA_B with Bowtie2 (3/4) [2012-10-31 14:51:47] Mapping left_kept_reads.m2g_um_seg4 to genome MaizeGDNA_B with Bowtie2 (4/4) [2012-10-31 15:54:52] Searching for junctions via segment mapping [2012-10-31 16:33:49] Retrieving sequences for splices [2012-10-31 16:35:22] Indexing splices [2012-10-31 16:36:25] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4) [2012-10-31 17:19:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4) [2012-10-31 18:13:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4) [2012-10-31 18:49:04] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4) [2012-10-31 19:01:19] Joining segment hits [2012-11-01 01:37:12] Reporting output tracks ----------------------------------------------- [2012-11-01 03:49:39] Run complete: 1 days 05:31:50 elapsed
I previously ran the same FASTQ/GTF with Tophat/Bowtie and had millions of mapped reads. Now I'm 0-for-2 with Tophat2.
Does anyone have any suggestions that might help recover an accepted_hits.bam file (other than going back to Tophat/Bowtie)?
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