User: Farhat
Farhat • 2.9k
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- Pune, India
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Posts by Farhat
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2
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... The output is in colorspace. You can use asid (Assembly Assistant for SOLiD) or denovo_postprocessor to convert it to basespace.
...
written 7.2 years ago by
Farhat • 2.9k
2
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1
answer
4.0k
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... Bowtie and BWA both index the genome and not the reads, so the RAM requirements are proportional to the genome size, and not the size of the FASTQ files. That aside, using single-end mode for paired end reads will give you more non-unique alignments since in case one of the pairs falls in a repeat r ...
written 7.5 years ago by
Farhat • 2.9k
2
votes
2
answers
1.4k
views
2
answers
... If you are dealing with SOLiD two-base encoded sequences, reverse complementing in base space is equivalent to simply reversing the sequence in color-space.
...
written 7.6 years ago by
Farhat • 2.9k
1
vote
1
answer
3.1k
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1
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Comment:
C: 7N Motif Search Over The Genome
... This is indeed a bit more complicated but can be solved with regular expressions. You can download the modified program at https://github.com/Farhat/patt_search You will have to enclose your patterns in quotes when using it on the command line to prevent shell from parsing braces.
...
written 7.7 years ago by
Farhat • 2.9k
2
votes
1
answer
2.5k
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1
answers
... No, it will be completely nonsensical most likely.
...
written 7.7 years ago by
Farhat • 2.9k
3
votes
1
answer
2.5k
views
1
answers
... It stands for colorspace fastq, the output from a SOLiD sequencer. For a brief primer check http://marketing.appliedbiosystems.com/images/Product_Microsites/Solid_Knowledge_MS/pdf/CSHL_Fu.pdf
...
written 7.7 years ago by
Farhat • 2.9k
1
vote
1
answer
3.1k
views
1
answers
Comment:
C: 7N Motif Search Over The Genome
... No, it will not work for general regular expressions. The expansion for N isn't supported but it is a minor change. I'll edit the program to include that.
...
written 7.7 years ago by
Farhat • 2.9k
0
votes
1
answer
1.7k
views
1
answers
... If you are using MEME there is an option to turn off reverse complimented motifs. There may be an option to do that there as well. Another option may be asking it to treat it as an amino acid sequence in which case there is no complimenting.
...
written 7.7 years ago by
Farhat • 2.9k
0
votes
1
answer
1.7k
views
1
answers
... If you reverse complement the motif from 16 it looks quite similar to the one from 15.
...
written 7.7 years ago by
Farhat • 2.9k
1
vote
2
answers
13k
views
2
answers
... It will start reporting from the position where there are alignments. If there are no reads aligned to the first position, it will not report them.
...
written 7.8 years ago by
Farhat • 2.9k
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