Hi all,
i'm dealing for the first time with Rna-seq data and i'm training performing some exercises running tophat on "wgEncodeCshlLongRnaSeqK562CellTotalFastqRep1.fastq" reads data from ENCODE project.
I'v issued the cocmmand "tophat -p 24 -G genes.gtf -o K562_1 hg19 reads.fastq" where genes.gtf is the transcript annotation file (hg19) from Illumina, hg19 is the reference genome (bowtie index) and reads.fastq is the single end reads file mentioned above (152 in length)
After 15 hrs i have in the output directory a very short .bam file (around 300 Kbyte).
Looking at the log files i find:
bowtie.left_kept_reads.fixmap.log:
::::::::::::::
# reads processed: 77046522
# reads with at least one reported alignment: 82 (0.00%)
# reads that failed to align: 77046440 (100.00%)
Reported 82 alignments to 1 output stream(s)
::::::::::::::
bowtie.left_kept_reads_seg1.fixmap.log
::::::::::::::
# reads processed: 77046440
# reads with at least one reported alignment: 17276886 (22.42%)
# reads that failed to align: 59283777 (76.95%)
# reads with alignments suppressed due to -m: 485777 (0.63%)
Reported 83222144 alignments to 1 output stream(s)
::::::::::::::
bowtie.left_kept_reads_seg2.fixmap.log
::::::::::::::
# reads processed: 77046440
# reads with at least one reported alignment: 22628110 (29.37%)
# reads that failed to align: 53761233 (69.78%)
# reads with alignments suppressed due to -m: 657097 (0.85%)
Reported 119440312 alignments to 1 output stream(s)
::::::::::::::
bowtie.left_kept_reads_seg3.fixmap.log
::::::::::::::
# reads processed: 77046440
# reads with at least one reported alignment: 18924892 (24.56%)
# reads that failed to align: 57402732 (74.50%)
# reads with alignments suppressed due to -m: 718816 (0.93%)
Reported 122913616 alignments to 1 output stream(s)
::::::::::::::
bowtie.left_kept_reads_seg4.fixmap.log
::::::::::::::
# reads processed: 77046440
# reads with at least one reported alignment: 12507630 (16.23%)
# reads that failed to align: 64207195 (83.34%)
# reads with alignments suppressed due to -m: 331615 (0.43%)
Reported 56082256 alignments to 1 output stream(s)
::::::::::::::
bowtie.left_kept_reads_seg5.fixmap.log
::::::::::::::
# reads processed: 77046440
# reads with at least one reported alignment: 19159264 (24.87%)
# reads that failed to align: 57337091 (74.42%)
# reads with alignments suppressed due to -m: 550085 (0.71%)
Reported 100864131 alignments to 1 output stream(s)
::::::::::::::
bowtie.left_kept_reads_seg6.fixmap.log
::::::::::::::
# reads processed: 77046440
# reads with at least one reported alignment: 7086758 (9.20%)
# reads that failed to align: 69837946 (90.64%)
# reads with alignments suppressed due to -m: 121736 (0.16%)
Reported 26553396 alignments to 1 output stream(s)
Moreover i find a lot (around 200) of "malformed closure" warnings in long_spanning_reads.log
Thanx a lot for any suggestions/advice.
i'm dealing for the first time with Rna-seq data and i'm training performing some exercises running tophat on "wgEncodeCshlLongRnaSeqK562CellTotalFastqRep1.fastq" reads data from ENCODE project.
I'v issued the cocmmand "tophat -p 24 -G genes.gtf -o K562_1 hg19 reads.fastq" where genes.gtf is the transcript annotation file (hg19) from Illumina, hg19 is the reference genome (bowtie index) and reads.fastq is the single end reads file mentioned above (152 in length)
After 15 hrs i have in the output directory a very short .bam file (around 300 Kbyte).
Looking at the log files i find:
bowtie.left_kept_reads.fixmap.log:
::::::::::::::
# reads processed: 77046522
# reads with at least one reported alignment: 82 (0.00%)
# reads that failed to align: 77046440 (100.00%)
Reported 82 alignments to 1 output stream(s)
::::::::::::::
bowtie.left_kept_reads_seg1.fixmap.log
::::::::::::::
# reads processed: 77046440
# reads with at least one reported alignment: 17276886 (22.42%)
# reads that failed to align: 59283777 (76.95%)
# reads with alignments suppressed due to -m: 485777 (0.63%)
Reported 83222144 alignments to 1 output stream(s)
::::::::::::::
bowtie.left_kept_reads_seg2.fixmap.log
::::::::::::::
# reads processed: 77046440
# reads with at least one reported alignment: 22628110 (29.37%)
# reads that failed to align: 53761233 (69.78%)
# reads with alignments suppressed due to -m: 657097 (0.85%)
Reported 119440312 alignments to 1 output stream(s)
::::::::::::::
bowtie.left_kept_reads_seg3.fixmap.log
::::::::::::::
# reads processed: 77046440
# reads with at least one reported alignment: 18924892 (24.56%)
# reads that failed to align: 57402732 (74.50%)
# reads with alignments suppressed due to -m: 718816 (0.93%)
Reported 122913616 alignments to 1 output stream(s)
::::::::::::::
bowtie.left_kept_reads_seg4.fixmap.log
::::::::::::::
# reads processed: 77046440
# reads with at least one reported alignment: 12507630 (16.23%)
# reads that failed to align: 64207195 (83.34%)
# reads with alignments suppressed due to -m: 331615 (0.43%)
Reported 56082256 alignments to 1 output stream(s)
::::::::::::::
bowtie.left_kept_reads_seg5.fixmap.log
::::::::::::::
# reads processed: 77046440
# reads with at least one reported alignment: 19159264 (24.87%)
# reads that failed to align: 57337091 (74.42%)
# reads with alignments suppressed due to -m: 550085 (0.71%)
Reported 100864131 alignments to 1 output stream(s)
::::::::::::::
bowtie.left_kept_reads_seg6.fixmap.log
::::::::::::::
# reads processed: 77046440
# reads with at least one reported alignment: 7086758 (9.20%)
# reads that failed to align: 69837946 (90.64%)
# reads with alignments suppressed due to -m: 121736 (0.16%)
Reported 26553396 alignments to 1 output stream(s)
Moreover i find a lot (around 200) of "malformed closure" warnings in long_spanning_reads.log
Thanx a lot for any suggestions/advice.
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