Originally posted by dpryan
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Hello D,
Sorry to trouble you again in this issue.
If I want to see whether a sequence (supposed named "GQ2") is expressed in bovine cells. I followed the solution in our last discussion: 'firstly I will generate the bowtie2 index of this "GQ2" based on the fasta sequence, and then map my fastq file to that "GQ2" genome.'
But when I did it, I got the error.
After I ran the bowtie2, it goes to the endless loop (obviously it is error). If I terminate the bowtie2, I found the error.
"bowtie2-align died with signal 2 (INT)"
I have googled the error but I didn't find any solution about this error. some post said it may due to memory problem but I don't think it is my problem. Hence I am wondering are my command lines wrong?
My step:
(1) generate the bowtie2 index of GQ2.
>GQ2
ATGGAGCACTTTCCCCGCTGTGTGCACGAGTCCTGGGGTTCCTCAAAGGA
GCCCCAGAAAACAGAGGTGCTGCAACTCTTGAGCTTAGCGGACCCTGAGG
.....
mkdir GQ2Bowtie2Index
cd GQ2Bowtie2Index
bowtie2 GQ2.fa GQ2
ls
GQ2.1.bt2 GQ2.2.bt2 GQ2.3.bt2 GQ2.4.bt2 GQ2.fa GQ2.rev.1.bt2 GQ2.rev.2.bt2
(2) map the gene on to 'GQ2' genome
bowtie2 --local --very-sensitive-local -p 8 ./GQ2Bowtie2Index/GQ2 -U bovine_sample1.fastq
then get the error!!!
I really don't know why I am wrong ...
Thank you!
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