CLC Genomics WB and the AMOS Bambus (developing Pipeline...)

[gabriel.lichtenstein]

Can AMOS Bambus build scaffolds with the CLC Genomics Workbench de novo assembly Contigs?

Cheers,

[DeNovoG]

Export your contig table as .ace.
Convert it with amos ace2contigs.
Generate your own mates files with a script.
run goBambus.

[sabrinaelias]

Can you please let me know how to generate .ace file from de novo assembly of CLC Assmbly cell?

[DeNovoG]

I am also trying to deal with that. Correct me if I am wrong, you want to use a multifasta file (assembly cell contigslist.fasta) and generate a .ace file?

I believe we require the mapping information of the reads to the contigs, I guess that clc assembly cell can generate a .cas file with that info as I saw in the manual, do you know something about this?

on the other hand we may wanna try this tool:

http://sourceforge.net/projects/fasta2ace/

Please let me know how it goes.

Cheers.

[sabrinaelias]

Hi DeNovoG
U r right. I want to convert a multifasta file to ace. Is it possible without a quality or alignment file?

Ya CLC assembly cell can generate a cas file with the reference assembly command but to convert that cas file to ace you will need the GUI form ie the genomic workbench to which I have no access.

Thanks for the link. I am sorry but I could not find any file there to download. is it moved? pls let me know if its wrong.

well I have found other fasa2ace perl scripts but they need alignment file in addition which I dont have from clc assembly cell output.

Thanks

[DeNovoG]

Hello,

well you were right about the link, I've sent an email to the author to see if he can fix it (https://sourceforge.net/users/crinkly_foil/)

whatever the tool I believe that to build a .ace file you will need the mapping information of you reads to your contigs.

how did you build your assembly? which type of data did you use, illumina, sanger, 454?

[catfisher]

Export your contig table as .ace.
Convert it with amos ace2contigs.
Generate your own mates files with a script.
run goBambus.

DeNovoG, do you have any script that can generate mates files? I have Illumina paired end reads in two files, I believe I can get the right .contig file from ace output, but I am not sure how to generate a right mates file based on the read. Hope you can help

[Bardj]

I am also wondering about this mate file script. I converted my clc ace output file to a contig file, but am struggling with the mate file.

Any tips would be greatly appreciated

[catfisher]

I am also wondering about this mate file script. I converted my clc ace output file to a contig file, but am struggling with the mate file.

Any tips would be greatly appreciated

I think the old thread would help you a lot. boetsie gave helpful information. http://seqanswers.com/forums/showthr...ghlight=bambus

[Bardj]

Thank you very much for redirecting me to that thread. I appreciate the help.

[gabriel.lichtenstein]

reply

This an example of what I used some time ago based on other thread here @ SeqAnswers (credit Boetsie please). Hope it helps:

#Step 1
#fastq 2 fasta:
for z in *.fastq
do perl fastqTofasta.pl $z
done


#Step 2
#300bpLib
for i in 300*fastq.fa; do cat $i |grep ">" |sed s/\>//g |sed 's/\/1*$/./g;s/\/2*$/./g'|awk -F "." '{print $1}' |sort |uniq -c |awk '{if ($1 == 1) print $2"/1\t"$2"/2\t300bpLib"}' > mates.$i.txt; done
#400bpLib
for e in 400*fastq.fa; do cat $e |grep ">" |sed s/\>//g |sed 's/\/1*$/./g;s/\/2*$/./g'|awk -F "." '{print $1}' |sort |uniq -c |awk '{if ($1 == 1) print $2"/1\t"$2"/2\t600bpLib"}' > mates.$e.txt; done


#Step 3
cat mates.* > my.mates


#Step 4
rm mates.*.txt
rm *.fa


#Source:
cat my.fasta |grep ">" |sed s/\>//g |sed 's/\/1*$/./g;s/\/2*$/./g'|awk -F "." '{print $1}' |sort |uniq -c |awk '{if ($1 == 2) print $2"/1\t"$2"/2\tsmall"}' > mates.txt

If you have two fasta files. Just insert one and change;
if ($1 == 2) to if ($1 == 1)
in the code, this way you only have to run it for one file

[catfisher]

gabriel.lichtenstein，did your contig data generated from CLC and mates file generated like you showed here work well? Would you mind sharing your bambus results here? like how you generated your .contig, how many contigs and what are the mates you used in your data? ect. I always got grommit script failure when I run bambus on my data, but I still can not figure it out. Thanks a lot.

[gabriel.lichtenstein]

Hi catfisher,

don't know if I will be able to help you but maybe you can get more info from your grommit error log:

I've seen you used this somewhere in your command line:
--append --logfile goBambus.log --debug 1

try something like this:
--append --logfile goBambus.log --debug 4

hope it helps