User: jaqx008
jaqx008 • 30
- Reputation:
- 30
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- New User
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- 2 days, 5 hours ago
- Joined:
- 9 months, 3 weeks ago
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Posts by jaqx008
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... Ok. where can I get tRNA sequences from please? ...
written 2 days ago by
jaqx008 • 30
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... So I used the vienna package and the structure I am getting doesnt represent all my sequences in my alignment file. its just a big circle with one sequence patched to one side of the circle. am I missing something? ...
written 4 days ago by
jaqx008 • 30
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... RNAalifold seem to be working. Thank you. ...
written 4 days ago by
jaqx008 • 30
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... I did see Vienna package and installed it. but have no idea how the usage is. I looked but didnt find the usage. Do you know it? ...
written 5 days ago by
jaqx008 • 30
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... Hello all,
I am trying to generate consensus RNA structures from a fasta output. I was going to use RNAforester to do it on the command line. I installed the RNAforester (the help menu shows up so I know I have it) but the usage is not giving me any output. I dont know if Im using it in the right wa ...
written 5 days ago by
jaqx008 • 30
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... Hello all.
I have a Transposable element bed file. it contains a list TEs in the format below; I want to split this bed file into two seperate beds with one containing class I TEs and the other class II TEs. In my understanding, class I TEs are retroelements while class two TEs are DNA associated m ...
written 25 days ago by
jaqx008 • 30
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... 1. Bowtie was already on this machine but I recently tried to upgrade it with brew. it works with original fasta before now.
2. Yes. Im currently running the bowtie on command line (terminal) and not with python. I was going to use the python later
3.
Example reads:
>Bf_V2_1:61669-61692
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... This still gave the `Segmentation fault: 11` error ...
written 4 weeks ago by
jaqx008 • 30
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... The fasta was generated as follows, bedtobam then bedtools getfasta to make fasta from bam. I dont understand what you mean by precompilled binary and compile from source. Also, I chose bowtie instead of bowtie2 because Im trying to map si and piRNA overlaps with a python script. ...
written 4 weeks ago by
jaqx008 • 30
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... Hello all.
I am trying to map some fasta files I generated from a TE.bed file. But I get the segmentation fault:11 error. some suggest its a memory problem and for that reason I tried to avoid outputting unaligned reads but it didnt help either. below is my command.
bowtie genome.index -f TE.fa ...
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