Hi,
today,I employed both bowtie and tophat to preform alignment of my RNA-seq data. I thought there must be a little difference between their result,however, both results were totally beyond my mind,here are my command as well as it's output
with the same data and genome)
bowtie command:
bowtie -p 6 --chunkmbs 200 -m 2 --sam crassa_reference -1 Dis3_f_QA_L1_1.fq -2 Dis3_f_QA_L1_2.fq f_aligned.sam
output:
# reads processed: 19798076
# reads with at least one reported alignment: 35 (0.00%)
# reads that failed to align: 19798041 (100.00%)
Reported 35 paired-end alignments to 1 output stream(s)
tophat command:
tophat -p 8 -G genes.gtf -o f_thout carssa_reference Dis3_f_QA_L1_1.fq Dis3_f_QA_L1_2.fq
tophat output:
# reads processed: 19797774
# reads with at least one reported alignment: 15504241 (78.31%)
# reads that failed to align: 4293396 (21.69%)
# reads with alignments suppressed due to -m: 137 (0.00%)
Reported 15605745 alignments to 1 output stream(s)
these outputs makes me confused ,any help would be greatly appreciate
today,I employed both bowtie and tophat to preform alignment of my RNA-seq data. I thought there must be a little difference between their result,however, both results were totally beyond my mind,here are my command as well as it's output

bowtie command:
bowtie -p 6 --chunkmbs 200 -m 2 --sam crassa_reference -1 Dis3_f_QA_L1_1.fq -2 Dis3_f_QA_L1_2.fq f_aligned.sam
output:
# reads processed: 19798076
# reads with at least one reported alignment: 35 (0.00%)
# reads that failed to align: 19798041 (100.00%)
Reported 35 paired-end alignments to 1 output stream(s)
tophat command:
tophat -p 8 -G genes.gtf -o f_thout carssa_reference Dis3_f_QA_L1_1.fq Dis3_f_QA_L1_2.fq
tophat output:
# reads processed: 19797774
# reads with at least one reported alignment: 15504241 (78.31%)
# reads that failed to align: 4293396 (21.69%)
# reads with alignments suppressed due to -m: 137 (0.00%)
Reported 15605745 alignments to 1 output stream(s)
these outputs makes me confused ,any help would be greatly appreciate
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