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Originally posted by Ben Langmead View PostI think the problem is that you're assuming -n 0 -l 16 is going to allow any alignment with no mismatches in the first 16 colors, but the -e limit also applies. -e also needs to be set high enough so that the sum of the quality values of all the mismatched positions in your example are still <= the -e limit. If no quality values are supplied, qualities all = 30.
Hope that helps. You may also want to consider using trimming (e.g. -3).
Thanks,
Ben
Now it works as I want
Best!
tomek
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Is it possible to get mapping quality and read quality (a single value per read, e.g. calculated out of base quality) for Bowtie?
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Originally posted by cp229 View PostHi Ben, I am a very new beginner with bowtie. I have a question about it, hope you can help me out. When I run bowtie with 454 long reads(the read length is about 200bp), the result is very weird that nearly 98% of reads are mismatching. (I tried human, yeast and e_coli). Could you tell me that whether I can use bowtie to align the long read or not....Thx
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Hi Ben, I am a very new beginner with bowtie. I have a question about it, hope you can help me out. When I run bowtie with 454 long reads(the read length is about 200bp), the result is very weird that nearly 98% of reads are mismatching. (I tried human, yeast and e_coli). Could you tell me that whether I can use bowtie to align the long read or not....Thx
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Hi, Ben Langmead
Recently I used bowtie to align some solexa reads in 100bp length. But the matched ratio is low. I want to know what's your recommendation for the option parameters for the long reads such as 100bp?
Thank you
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calling variants with samtools after bowtie -- very long lines in output
Hi,
I am facing the following situation. It looks like there could be an error in my approach, but I am trying to figure out. I would much appreciate your inputs/suggestions to resolve my problem.
1. (PROBLEM) I am trying to align PhiX-174 reads, obtained from GA IIx, on to the reference (from NCBI) using the bowtie program and then subsequently look for variants using samtools.
I am getting very long lines in the final SNP calling output file and the result doesn't look meaningful.
2. Illumina-analysis-software-generated fastq file, which I am using contains some 18 million read sequences.
3. If needed, I can provide a truncated version of the output, as the output is 366M in size.
4. To check the Bowtie installation on my computer, I ran the example provided in the Bowtie: Tutorial section, especially, Finding variations with samtools -- the run was successful.
I performed the following steps:
STEP #1: Generate Indexes for the PhiX-174 genome
bowtie-build phix174.fasta phix174
STEP #2: Perform alignment with bowtie and generate sam file
bowtie -S phix174 phix174.fastq phix174.sam
STEP #3: Convert sam to bam file
samtools view -bS -o phix174.bam phix174.sam
STEP #4: Sort the bam file in preparation for SNP calling
samtools sort phix174.bam phix174.sorted
STEP #5: Identify SNPs...
samtools pileup -cv -f phix174.fasta phix174.sorted.bam > phix174.variants
Thanks,
Issaac
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Originally posted by didymos View PostHowever in my reads from SOLiD I have reads of length 35 so this miRNA is longer and is:
T31210212010221212202033002010303111
but first 23 "numbers" are the same so using this option:
bowtie -a -n 0 -l 16 -C ../mouse/miRNA-stem-loop -c T31210212010221212202033002010303111
I should be able to map this read, but it does not work like this:
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments
and I have no idea why...
Thank you for any sugestions!
Hope that helps. You may also want to consider using trimming (e.g. -3).
Thanks,
Ben
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bowtie view? I'm confused - can you send the exact command you're using?
Thanks,
Ben
Originally posted by afadda View Posthi. i get segmentation fault only when I run bwotie view on a certain data. it always stops at the same genome coordinates, whether it's in one big file with all chromosomes in, or just a file of that particular chromosome. can't tell what the problem is. help!!
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hi. i get segmentation fault only when I run bwotie view on a certain data. it always stops at the same genome coordinates, whether it's in one big file with all chromosomes in, or just a file of that particular chromosome. can't tell what the problem is. help!!
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problem with SOLiD data mapping
Hi,
I am trying to map short reads from SOLiD into indexes generated from stem-loop sequences of miRs to get information about miRNA in my samples.
Indexes I have generated from fasta file (from miRBASE) by bowtie-build -C and it works great. However I have some problem with mapping... I will explain it with example:
mmu mir-378 -> ACTGGACTTGGAGTCAGAAGG
when I have converted it into colorspece (with T at the begining - from promotor) I got:
T312102120102212122020
Mapping this miRNA works great:
bowtie -a -n 0 -C ../mouse/miRNA-stem-loop -c T312102120102212122020
0 + mmT-mir-378 43 CTGGACTTGGAGTCAGAAG qqqqqqqqqqqqqqqqqqq 0
However in my reads from SOLiD I have reads of length 35 so this miRNA is longer and is:
T31210212010221212202033002010303111
but first 23 "numbers" are the same so using this option:
bowtie -a -n 0 -l 16 -C ../mouse/miRNA-stem-loop -c T31210212010221212202033002010303111
I should be able to map this read, but it does not work like this:
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments
and I have no idea why...
Thank you for any sugestions!
Best
tomek
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Hi Ben,
I appreciate your quick response.
I think I understood it.
Thanks,
Corthay
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Hi Corthay,
Originally posted by corthay View PostI would like to ask about "-n" option. I would like to map read
following conditions.
1. first N bases must be perfect match.
2. reported position must be 'best' hit.
I used " -n 0 -l N -a --best --strata ". I am wondering if the '--best'
option is only guaranteed "-n" and '-l' option. For example, I worry
that bowtie reports 1 mismatch hit even if there is perfect hit.
Originally posted by corthay View PostAlso, I would like to know the option to get random position if reads hit to multiple position.
Thanks,
Ben
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Question abou "-n" option.
Hi,
I would like to ask about "-n" option. I would like to map read
following conditions.
1. first N bases must be perfect match.
2. reported position must be 'best' hit.
I used " -n 0 -l N -a --best --strata ". I am wondering if the '--best'
option is only guaranteed "-n" and '-l' option. For example, I worry
that bowtie reports 1 mismatch hit even if there is perfect hit.
Also, I would like to know the option to get random position
if reads hit to multiple position.
Thanks,
Corthay.
Leave a comment:
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