User: Farhat

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Farhat2.9k
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Location:
Pune, India
Website:
http://www.iiserpune.a...
Last seen:
4 years, 7 months ago
Joined:
9 years, 4 months ago
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Posts by Farhat

<prev • 114 results • page 1 of 12 • next >
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Answer: A: What Format Are The Results Of A Colorspace Assembly Using Velvet (Velvetg_De) I
... The output is in colorspace. You can use asid (Assembly Assistant for SOLiD) or denovo_postprocessor to convert it to basespace. ...
written 6.5 years ago by Farhat2.9k
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Answer: A: Aligning Paired-End Reads In Single-End Mode
... 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 6.8 years ago by Farhat2.9k
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Answer: A: Anybody Needs Just Reverse (Not Reverse Complement) Action?
... 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 6.9 years ago by Farhat2.9k
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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 7.0 years ago by Farhat2.9k
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Comment: C: Trinity - Type Of Reads: ( Cfa, Cfq, Fa, Or Fq )
... No, it will be completely nonsensical most likely. ...
written 7.0 years ago by Farhat2.9k
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Answer: A: Trinity - Type Of Reads: ( Cfa, Cfq, Fa, Or Fq )
... 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 7.0 years ago by Farhat2.9k
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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 7.0 years ago by Farhat2.9k
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Comment: C: Minor Size Differences Leading To Major Motifs Differences
... 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 7.0 years ago by Farhat2.9k
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Answer: A: Minor Size Differences Leading To Major Motifs Differences
... If you reverse complement the motif from 16 it looks quite similar to the one from 15. ...
written 7.0 years ago by Farhat2.9k
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Comment: C: Coverage In Bam File - Bases And Overall Count
... 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 7.1 years ago by Farhat2.9k

Latest awards to Farhat

Popular Question 5.1 years ago, created a question with more than 1,000 views. For Strange Fastqc Report
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Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: Transcription Factor Binding Sites Database For Bacteria?
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Aligning Colorspace Reads Using Bwa
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: How To Interpret -D File In Samtools Variant Calling Pipeline?
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Appreciated 5.7 years ago, created a post with more than 5 votes. For A: Counting Repeat Sequence
Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: Best Database Of Transcription Factor Binding Sites
Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: Convert Part Of A Bam File To Sam
Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: Latest High Thoughput Figures
Appreciated 5.7 years ago, created a post with more than 5 votes. For Which Version Control System Is Most Common For Bioinformatics?
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Converting Gbff To Gff3
Appreciated 5.7 years ago, created a post with more than 5 votes. For C: Tools For Validating Blast Result?

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