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  • JonB
    replied
    Could you run a program like Cufflinks specifying a mean transcript length of about 18 nts, and then get a gtf file of the different transcripts?

    Leave a comment:


  • sBeier
    replied
    Usually, with small RNAs being not bigger than 24 nt, you would filter for reads between maybe 15 - 28 nt length. Those are the complete transcripts, so no need for any assembly.

    Leave a comment:


  • JonB
    replied
    Originally posted by yjhua2110 View Post
    in our deepBase database, we use options: –k 200 –v 0. the Specifying the parameters (–k 200 –v 0) instructs Bowtie to report up to 200 perfect hits for each read.

    deepBase is a platform for annotating and discovering small and long ncRNAs from next generation sequencing data. It is available at http://deepbase.sysu.edu.cn
    I am mapping reads from a small RNA sequencing, and I am curious how you treat the results after mapping with the -k 200 option? Do you assemble the transcripts? Or do you report all the locations where a read has been mapped?
    Last edited by JonB; 06-10-2013, 05:26 AM. Reason: lacked quote

    Leave a comment:


  • unique379
    replied
    Dear all,

    as above discussions and suggestion, could i use bowtie something like this for miRNA alignment ?? just please make me sure.

    bowtie --sam -q -n 0 -l 15 -e 99999 -k 200 -a --chunkmbs 1024 --best ....

    Leave a comment:


  • zeam
    replied
    No mismatch allowed

    Originally posted by NicoBxl View Post
    did you allow mismatches in your alignment ?
    What I want is to dissect the correlation between smRNA and DNA methylation.Previous studies reveals that both of miRNA and siRNA involed in DNA methylation.The problem I met is 1)mapping;2)separating miRNA and siRNA from smRNA-seq data.Can you give me some suggestions if you have some experience on these subjects?

    Leave a comment:


  • NicoBxl
    replied
    did you allow mismatches in your alignment ?

    Leave a comment:


  • zeam
    replied
    Hi everyone,
    When you were processing smRNA-seq data,which software did you use?I have attempted SOAP2 and bowtie,both of them didn't work well enough,many of the reads could not map to the reference.But when I used blat,it works well except consuming time.Can you guys give me some suggestions?My data is from plants,and I want to sepate miRNA and siRNA from smRNA-seq data.
    Thanks!

    Leave a comment:


  • jdanderson
    replied
    Hello Everyone,

    I would like to second mgogol's suggestion. It is part of a larger set of tools called FASTX Toolkit: http://hannonlab.cshl.edu/fastx_toolkit/index.html

    I've found the tools to be very useful and user friendly.

    Cheers,
    Johnathon

    Leave a comment:


  • mgogol
    replied
    fastx_clipper can trim adapter sequence.

    Leave a comment:


  • dukevn
    replied
    Originally posted by didymos View Post
    Hi,

    In Bowtie you can trim n nucleotides from 3' or 5' end with -3 n or -5 n option - so you can play with this and -v 2 for two mm. However for trimming I am using blast with smaller word size -W option, and then choosing only those mappings which are on the 3' end.

    tomek
    Thanks, but I want to trim the adapter sequence, not n nucleotides.

    Leave a comment:


  • didymos
    replied
    Hi,

    In Bowtie you can trim n nucleotides from 3' or 5' end with -3 n or -5 n option - so you can play with this and -v 2 for two mm. However for trimming I am using blast with smaller word size -W option, and then choosing only those mappings which are on the 3' end.

    tomek

    Leave a comment:


  • dukevn
    replied
    Anybody knows how I can trim out the adapter sequence with a certain number of mismatch (1 or 2)?

    Thanks,

    D.

    Leave a comment:


  • yjhua2110
    replied
    Originally posted by whsqwghlm View Post
    Each read may map exactly to many places in the genome. We want to capture all of these locations to a threshold promiscuity, typically 100, over which we discard all of the mappings (i.e. if 101 alignments are returned from the search).
    you can use the options: -a -m 100. Specifying -m 100 instructs bowtie to refrain from reporting any alignments for reads having more than 100 reportable alignments.

    Leave a comment:


  • whsqwghlm
    replied
    Each read may map exactly to many places in the genome. We want to capture all of these locations to a threshold promiscuity, typically 100, over which we discard all of the mappings (i.e. if 101 alignments are returned from the search).

    Leave a comment:


  • didymos
    replied
    I am new in the miRNA field and I am wondering why you are using -k 200 or 101 option? In other words why you want to have 200 alignment with 0 mismatches, rather than one unique with 0 mm?
    Thanks!

    tomek

    Leave a comment:

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