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Old 10-03-2014, 12:34 PM   #1
dolbi
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Location: NYC

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Red face bismark can't get work with test data

PHP Code:
bismark_v0.12.5/bismark_genome_preparation --path_to_bowtie ~/scripts/bowtie-1.1.0/ --verbose .
bismark_v0.12.5/bismark -n 1 -l 50 --path_to_bowtie ~/scripts/bowtie-1.1.0/ ~/ngs/bismark-hsatest_data.fastq 
These were the two code I tried with the bismark. While I didn't get any sequences that were aligned with the genome.

The genome sequence are in a fasta file hg19.fa, if anything, the working directory when I prepare the genome don't have this file, but have a link to hg19.fasta in other folder.

This is a part of the report:

Quote:
Final Alignment report
======================
Sequences analysed in total: 10000
Number of alignments with a unique best hit from the different alignments: 0
Mapping efficiency: 0.0%

Sequences with no alignments under any condition: 10000
Sequences did not map uniquely: 0
Sequences which were discarded because genomic sequence could not be extracted: 0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT: 0 ((converted) top strand)
CT/GA: 0 ((converted) bottom strand)
GA/CT: 0 (complementary to (converted) top strand)
GA/GA: 0 (complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total: 0
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Old 10-30-2014, 06:15 PM   #2
homeuser1
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Location: alabama

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Default bismark bug

Hi,

I faced similar problem. Have u solved it? Thanks
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Old 10-31-2014, 01:52 PM   #3
dolbi
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Default

Quote:
Originally Posted by homeuser1 View Post
Hi,

I faced similar problem. Have u solved it? Thanks
This turns out something is wrong when I building the genomic database. Basically, I made the index with default bowtie program which is bowtie2, and when aligning I asigned with bowtie1 program. This means I am using bowtie1 aligning with a database build up with bowtie2. The program is not giving any warning or error.

I hope this can helpful to you.
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Old 11-01-2014, 01:54 AM   #4
fkrueger
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Location: Cambridge, UK

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Default

Quote:
Originally Posted by dolbi View Post
This turns out something is wrong when I building the genomic database. Basically, I made the index with default bowtie program which is bowtie2, and when aligning I asigned with bowtie1 program. This means I am using bowtie1 aligning with a database build up with bowtie2. The program is not giving any warning or error.

I hope this can helpful to you.
Sorry, but this incorrect. The default for both the genome preparation as well as the aligner is Bowtie (Bowtie 2 requires the flag --bowtie2 in both cases). Also, if the specified genome folder doesn't contain files with the required file extension it will die with an warning message and prompt you to run the correct genome preparation first. If all files are present there is still a chance that the indexing left corrupt files, e.g. if it got killed or terminated due to memory issues or the like.

If the test data report shows no aligned files you need to look at the on-screen text (or the error log) for clues what went wrong. I am happy to help trouble shooting if you can send me the error log.
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