I used KAligner, abyss2afg and bank-transact to generate an amos bank from my ABySS assembly (without any problem).
I tried to run amosvalidate, but in the step 300 (Analyzing mate-pairs), but I had the message "No library account found in bank out.bnk". Indeed, there is no file "LIB.*" in the bank directory…
Why these files are not present? Is it possible to use this pipeline with an ABySS assembly ?
Thank you in advance for your help!
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Hi,
Do you suspect there is no LIB partition because they was a problem parsing the input? or because your sequence data is not paired? If your data is not paired, you can simply comment out that step of the pipeline to avoid the error. If your data is paired, then you'll have to find a way to add the pairing information to your bank. This is typically done with the toAmos converter, but I'm not as familiar with abyss2afg.
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Hi,
First, thank you for your reply.
In fact, my data are paired. But with abyss, I have only reads and contigs in fasta format. Maybe this is not enough to have a complete bank ? (I noticed that the edge account, the contig link account and the scaffold information were also missing…)
I believe that data in fasta format does not suffice for using toAmos, does it?
Best regards
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toAmos will work with just fasta, but will leave many of the data types unpopulated. You need to explicitly include the pairing information when you load the bank. Usually this is done using 'toAmos', which can read pairing information - usually with the '-m' option.
There has been some work recently on new converters, but I've lost track of who was doing what. You might get more feedback if you email the amos-help mailing list (amos-help@lists.sourceforge.net). That has a wider readership than this forum. There may be a converter in the CVS tip that isn't in the official release yet that may help you out if you can describe the kind of data formats you are dealing with.
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Thank you for your help, finally, I managed to use amosvalidate with the bank generated as indicated following:
KAligner -seq -mk <k> <reads> <contigs> | abyss2afg -m <mean>-s <sd> <contigs> - > out.afg
bank-transact -cb out.bnk - out.afg
(read must be named as foo/1 and foo/2)
The OVL and LAY files are absent but not useful.
For those interested, there are a few changes to the pipeline amosvalidate:
1. We must remove the "-scaff" option in steps 300, 310 and 320. (which need scaffold information)
2. We must comment on the steps 600 to 710 and from 1010 to 1020. (which need singleton information)
Best regards
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I used KAligner, abyss2afg and bank-transact to generate an amos bank from my ABySS assembly (without any problem).
I tried to run amosvalidate, but in the step 300 (Analyzing mate-pairs), but I had the message "No library account found in bank out.bnk". Indeed, there is no file "LIB.*" in the bank directory…
Why these files are not present? Is it possible to use this pipeline with an ABySS assembly ?
Thank you in advance for your help!
Hi,
Do you suspect there is no LIB partition because they was a problem parsing the input? or because your sequence data is not paired? If your data is not paired, you can simply comment out that step of the pipeline to avoid the error. If your data is paired, then you'll have to find a way to add the pairing information to your bank. This is typically done with the toAmos converter, but I'm not as familiar with abyss2afg.
Hi,
First, thank you for your reply.
In fact, my data are paired. But with abyss, I have only reads and contigs in fasta format. Maybe this is not enough to have a complete bank ? (I noticed that the edge account, the contig link account and the scaffold information were also missing…)
I believe that data in fasta format does not suffice for using toAmos, does it?
Best regards
toAmos will work with just fasta, but will leave many of the data types unpopulated. You need to explicitly include the pairing information when you load the bank. Usually this is done using 'toAmos', which can read pairing information - usually with the '-m' option.
There has been some work recently on new converters, but I've lost track of who was doing what. You might get more feedback if you email the amos-help mailing list (amos-help@lists.sourceforge.net). That has a wider readership than this forum. There may be a converter in the CVS tip that isn't in the official release yet that may help you out if you can describe the kind of data formats you are dealing with.
Hi,
Thank you for your help, finally, I managed to use amosvalidate with the bank generated as indicated following:
KAligner -seq -mk <k> <reads> <contigs> | abyss2afg -m <mean> -s <sd> <contigs> - > out.afg
bank-transact -cb out.bnk - out.afg
(read must be named as foo/1 and foo/2)
The OVL and LAY files are absent but not useful.
For those interested, there are a few changes to the pipeline amosvalidate:
1. We must remove the "-scaff" option in steps 300, 310 and 320. (which need scaffold information)
2. We must comment on the steps 600 to 710 and from 1010 to 1020. (which need singleton information)
Best regards