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Forum: Bioinformatics 12-19-2015, 06:28 PM
Replies: 38
Views: 7,145
Posted By entomology
Yes, that's does work. And it's more flexible and...

Yes, that's does work. And it's more flexible and robust with different situations. Thank you for the great work. I've got a lot of fantastic script in bbmap!
Forum: Bioinformatics 12-19-2015, 03:39 PM
Replies: 38
Views: 7,145
Posted By entomology
Thank you for your great work. I've tried the...

Thank you for your great work. I've tried the script with below two fasta files.

a.fasta

>1
aaaaaa
>2
tttttt
>3
gggggg
Forum: Bioinformatics 12-18-2015, 10:18 PM
Replies: 38
Views: 7,145
Posted By entomology
Another good method, thank you.

Another good method, thank you.
Forum: Bioinformatics 12-18-2015, 10:13 PM
Replies: 38
Views: 7,145
Posted By entomology
Yes, this time it works though the output is not...

Yes, this time it works though the output is not as expected :).

more out.fas
>1123-11234
--
gggggg
>13424241234-23423
>1123-11234
aaaaaa
ctaacg
Forum: Bioinformatics 12-18-2015, 10:06 PM
Replies: 38
Views: 7,145
Posted By entomology
Admire you with the enthusiasm on programming,...

Admire you with the enthusiasm on programming, which makes an excellent programmer. Different running environment makes tons of unexpected problems that's why a robust code is really not easy to...
Forum: Bioinformatics 12-18-2015, 01:23 PM
Replies: 38
Views: 7,145
Posted By entomology
Thank you very much for your help. you are right,...

Thank you very much for your help. you are right, i get the order wrong. now it works really good with the updated version without warning.

the command test gives the result as below:

perl -v
...
Forum: Bioinformatics 12-18-2015, 12:58 PM
Replies: 38
Views: 7,145
Posted By entomology
I'm using centos ...

I'm using centos

2.6.32-573.7.1.el6.centos.plus.x86_64

when i change as you recommended, this time I got result. but still with some error and the result seems not as expected.
...
Forum: Bioinformatics 12-18-2015, 12:42 PM
Replies: 38
Views: 7,145
Posted By entomology
I've got below message when I running the script,...

I've got below message when I running the script, do i miss some module?

Can't locate object method "getline" via package "IO::Handle" at ./fetch_fasta.test line 30
Forum: Bioinformatics 12-18-2015, 12:37 PM
Replies: 38
Views: 7,145
Posted By entomology
Forgive my poor programming skill, still I got...

Forgive my poor programming skill, still I got some error message as below

-bash: syntax error near unexpected token `do'
Forum: Bioinformatics 12-18-2015, 12:31 PM
Replies: 38
Views: 7,145
Posted By entomology
Actually, I've deal with some small rna sequence...

Actually, I've deal with some small rna sequence which is with length of 18-30. Anyway, thank you for your kindness.
Forum: Bioinformatics 12-18-2015, 12:25 PM
Replies: 38
Views: 7,145
Posted By entomology
I've upload the two file, the expected output is...

I've upload the two file, the expected output is like this:

>1123-11234
aaaaaa
>232-23424
tttttt
>416-2
gggggg
>13424241234-23423
cccccc
Forum: Bioinformatics 12-17-2015, 02:03 PM
Replies: 38
Views: 7,145
Posted By entomology
Thank you for the code. It can change my...

Thank you for the code. It can change my sequences to fasta file. And I try bbduk.fas again, but the result is not as expected. An example will be more easier to understand. there are two fasta
...
Forum: Bioinformatics 12-17-2015, 01:00 PM
Replies: 38
Views: 7,145
Posted By entomology
Yes, I've tried bbduk.sh. bbduk.sh in=a.fa...

Yes, I've tried bbduk.sh.

bbduk.sh in=a.fa ref=b.fa out=c.fa mkf=1 mm=f k=31

But my situation is that b.fa is not fasta file, it contain one sequence per line. I just want the sequence in b...
Forum: Bioinformatics 12-17-2015, 11:39 AM
Replies: 38
Views: 7,145
Posted By entomology
No worry, I'll try to use grep to deal with the...

No worry, I'll try to use grep to deal with the problem :).
Forum: Bioinformatics 12-17-2015, 10:48 AM
Replies: 38
Views: 7,145
Posted By entomology
Actually, I do more wet lab most of the time....

Actually, I do more wet lab most of the time. Sometimes, I'll also do simple small rna analysis with ready-to-use perl script and simple shell script. It's enough most of the time with my work, but...
Forum: Bioinformatics 12-17-2015, 07:49 AM
Replies: 38
Views: 7,145
Posted By entomology
Seems these script also deal with a list of ids,...

Seems these script also deal with a list of ids, then using these ids to fetch sequences in a fasta file. I wanna use sequences directly and get a subset of fasta from a big fasta file base on...
Forum: Bioinformatics 12-17-2015, 01:27 AM
Replies: 38
Views: 7,145
Posted By entomology
Actually, I do prefer command based under shell...

Actually, I do prefer command based under shell environment. grep seems a great way to do it, thanks for tips.
Forum: Bioinformatics 12-17-2015, 01:20 AM
Replies: 38
Views: 7,145
Posted By entomology
3xs for the info.

3xs for the info.
Forum: Bioinformatics 12-16-2015, 03:44 PM
Replies: 38
Views: 7,145
Posted By entomology
Extract multiple fasta sequences from a fasta file based on sequenes

I've searched in the forum and google as well, but most of cases are extract sequences from fasta file based on id list. but now I only have several sequences without ids and i want to extract from a...
Forum: Bioinformatics 07-12-2012, 03:59 PM
Replies: 5
Views: 4,656
Posted By entomology
Thank you all the same!

Thank you all the same!
Forum: Illumina/Solexa 07-11-2012, 04:13 PM
Replies: 2
Views: 1,191
Posted By entomology
3xs for your reply, I'll try R program.

3xs for your reply, I'll try R program.
Forum: Bioinformatics 07-11-2012, 04:12 PM
Replies: 5
Views: 4,656
Posted By entomology
thanks, I'll try to learn basic perl first, parse...

thanks, I'll try to learn basic perl first, parse with fasta is first step, maybe bioperl is more easy to handle.
Forum: Bioinformatics 07-11-2012, 08:21 AM
Replies: 5
Views: 4,656
Posted By entomology
how to get specific length sequence from a fasta file

I'm not so familiar with perl, is there script can fetch specific length of sequence from a fasta file? many thanks!
Forum: Illumina/Solexa 07-11-2012, 05:53 AM
Replies: 2
Views: 1,191
Posted By entomology
how to make this kind of mapping figure

I've used mirDeep2 to mapping small rna to reference genome and get corresponding data. But I don't know how to making figure like below with these data. could andboy help? 3xs in advance.
...
Forum: Bioinformatics 07-08-2012, 10:32 AM
Replies: 0
Views: 1,536
Posted By entomology
fastx_clipper remove more than I want to remove

I want to remove 3' adapter of small rna sequencing data generated from illumina.

first, I try mapper.pl within mirdeep2 toolkit. but soon i found it can't remove the unclipped sequence.

so I...
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