Isn't there a feature to export unmapped reads to a file?
I always run bowtie and export unmapped and repeats using
--unfq unaligned.fastq --maxfa duplicates.fastq
taking a look at the size of both files compared to your original file gives you an approx idea of % unaligned/repeats
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Hi tianell,
Originally posted by tianell View PostWhen I align certain short reads to reference using Bowtie, can I get a result message related to none-matched case??
I could not find an option to get a such result message.
I want to report even if certain short reads are not aligned to reference in order to use this information(not aligned!).
Thanks,
Ben
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Ben, help me..
Hi Ben,
I have a question for you about alignment result message.
When I align certain short reads to reference using Bowtie, can I get a result message related to none-matched case??
I could not find an option to get a such result message.
I want to report even if certain short reads are not aligned to reference in order to use this information(not aligned!).
I wil wait your answer, Ben. Thank you so much.
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Thanks
Hi Ben,
Thanks for your advice. There were many 'N's in simulated data, so that they may interrupt paired-mapping. I'll try with other data sets. Thanks.
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Originally posted by Wind View PostBowtie is a nice tool for short read alignment I think. However, I found a problem in pair-end data mapping. I produced 75bp reads by simulating Illumina's high-throughput sequencing, and aligned them to the reference sequence. By the way, only few alignments, less than 10, are reported. As 1300000 alignments are reported with non paired-end mapping, probably it is wrongly mapped I think.
My option is "bowtie -p 8 -a -y -X 650 human -1 reads_1.fa -2 reads_2.fa output.map".
Thanks,
Ben
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Bowtie is a nice tool for short read alignment I think. However, I found a problem in pair-end data mapping. I produced 75bp reads by simulating Illumina's high-throughput sequencing, and aligned them to the reference sequence. By the way, only few alignments, less than 10, are reported. As 1300000 alignments are reported with non paired-end mapping, probably it is wrongly mapped I think.
My option is "bowtie -p 8 -a -y -X 650 human -1 reads_1.fa -2 reads_2.fa output.map".
Can anybody tell me what is the problem?Last edited by Wind; 08-03-2009, 03:35 AM.
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Ben,
I used the latest version 0.10.1 and it still hangs. It seems to complete the job (or almost, I haven't verified that fact yet) and stops writing to the output file but then it never closes.
Do you want me to run the debug version or try the extra flags again?
Chuck
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Hi Ben,
I've been teaching and not working on the data lately. I will give it a try soon.
I have a question for you about assembly quality evaluation, in two contexts.
1) to simply evaluate the quality of the assembly of the short reads against the reference sequences, beyond simple coverage
2) when there are actual differences between the sequenced genome and the reference genome, in finding indels and whatnot
I am looking AMOS, which seems to be one of the few that provide some kind of quality score for the assembly. Are you aware of others?
I am trying to quickly narrow my analysis down to those de novo contigs with good assembly scores. I proposed a simple metric in a manuscript and the reviewer suggested I use other 'standard' measures but gave no pointers as to which ones I should be using. Things are changing so fast it is hard to keep track of the 'standard'...
Thanks,
Chuck
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Originally posted by seq_GA View PostAnd hence any suggestions to increase the mapping rate of Bowtie using -n options?
Thanks,
Ben
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Originally posted by Ben Langmead View PostProbably the -e limit again. See my previous post.
Ben
I am trying to get as many mapping as eland reports and trying to play around with Bowtie's parameters.
As you had suggested earlier, I tried using -e till 2000 to increase the mapping as good as eland but still Bowtie misses a lot of mappings when compared to eland.
-v option would give a comparable results ( I tested for read length 28 which is also the seed length) as eland but with the increasing number of Ns in the 3`end, it would be good to use -n option and try to allow any number of mismatches beyond seed length.
And hence any suggestions to increase the mapping rate of Bowtie using -n options?
Thanks.
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Hi Chuck,
Originally posted by chuck View PostI tried bowtie remade with extraflags but it just did the same thing. Would there be a log file somewhere or something in the map file? I can't seem to find any additional output.
Thanks,
Ben
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Originally posted by Ben Langmead View PostBowtie will index and align against references containing non-A/C/G/T characters, but alignments overlapping non-A/C/G/T characters in the reference are invalid and won't be reported.
Out of curiosity, what's the behavior you would like? E.g. if a C in a read were to align against a Y in the genome, would you like that to be considered a match, incurring no penalty against the alignment?
Thanks,
Ben
So our preferred behavior would be to not penalise either the C or T (if the reference contained a Y at this position)
Anyway I find bowtie very useful, thanks for all your work!
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Originally posted by seq_GA View PostCan you please explain me why there are more number of mapping when -v 2?
Ben
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Originally posted by seq_GA View Postwith -v 3, Bowtie is also reporting one mapping location.
I want to use seedlength as 28(default) with 2 mismatches. hence I used -n 2 since I am comparing eland_28 and Bowtie results.
But still why Bowtie is not reporting?
Ben
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Hi Ben,
I did a quick comparison on with -v 2 and -n 2.
The reads are 35bps length and i used -3 6 to trim 3` sequences and hence my mappabale reads would be 28 in size in order for me to compare eland_28 results.
Code:bowtie -a -m 10 -v 2 --strata --best --solexa-quals -p 15 -3 ../../Genome/hg18/hg18 ../s_1_sequence.txt out_aln.txt
When I look at the unque ly mapped tags with -v 2 is more than with -n 2.
Can you please explain me why there are more number of mapping when -v 2?
Thanks.
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