User: Bob Harris

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Bob Harris190
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Posts by Bob Harris

<prev • 21 results • page 1 of 3 • next >
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Answer: A: Troubles with full settings on Lastz
... Another thought.  You could try appending some unique sequence to both the reference and the queries before alignment.  For example, appending "ACGTACGTACGT" as a prefix should make the alignment extend past any error near the left end of the real sequence. I just tried that (command line), using t ...
written 2.5 years ago by Bob Harris190
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Answer: A: Troubles with full settings on Lastz
... I've tried the example sequences with command line lastz and it looks like the problem is that galaxy must be using an older version of lastz. A change made in lastz version 1.03.00 improves the tolerance for mismatches and indels near the end of reads. Specifically, version 1.03.00, with your para ...
written 2.5 years ago by Bob Harris190
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Answer: A: Troubles with full settings on Lastz
... Howdy, Edouard,   I've tried to reproduce this failure using command-line lastz and was unable to. Specifically, I created a random 39nt sequence as my target sequence, then created two 100nt sequences with the 39nt sequence embedded at positions 1..39 and at 2..40.  I ran lastz with the 39nt seq ...
written 2.5 years ago by Bob Harris190
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Curious-- What Does "You Are Currently Viewing A Deleted History!" Mean?
... Howdy, A couple weeks ago I popped up main.g2.bx.psu.edu and, without logging in, submitted a small megablast job, then forgot about it. Today I remembered that job and went back to look at it. The results are there (hurray!) but I am confused by the notification that "You are currently viewing a ...
written 5.1 years ago by Bob Harris190
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Comment: C: Run Bowtie To Estimate Mean Inner Distance Between Mate Pairs
... Howdy Jianguang, There's a more complete description of the SAM format in "The Sequence Alignment/Map format and SAMtools", Li et al, Bioinformatics (2009). And you can find the latest specification for the format at samtools.sourceforge.net . In the spec, the terminology for the ISIZE field has b ...
written 5.3 years ago by Bob Harris190
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Answer: A: Bx.Seq.Twobit - Write A 2Bit File?
... Howdy, Amit, For my personal use, I have always used faToTwobit to create 2bit files. I wrote most of the original seq module in bx-python (circa 2005?), adapting it from a nib format reader that James Taylor wrote. The main goal at the time was to read DNA from a variety of sequence file formats ...
written 5.9 years ago by Bob Harris190
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Answer: A: Lastz Very Slow
... Howdy, Andrew, One possibility is that there are more jobs on the cluster. I'm not familiar enough with the galaxy interface to know if there's an easy way to tell how much time the job sits on the cluster's queue waiting and how much time the job is actually running. Assuming there's no cluster ...
written 6.0 years ago by Bob Harris190
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Comment: C: Selecting Reads At Random From Fastq File
... David, in my experience with Illumina sequencing, it looks like the reads at the start of a file have a much higher sequencing error rate. Bob H ...
written 6.1 years ago by Bob Harris190
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Comment: C: Fastq Groomer
... Howdy, Rich, My interpretation of the error report is that the fastq file you are trying to groom contains the indicated text (lab/solexa_public/Zon/ 111021_WICMT-SOLEXA_64KF7AAXX/QualityScore/s_3_1_sequence.txt) on a line where it expects a valid fastq header. I believe a valid header line would ...
written 6.1 years ago by Bob Harris190
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Comment: C: Aligning Long Reads
... Shalabh, Not to toot my own horn, but I believe lastz should do a better job than bwa for reads longer than about 100 bp. bwa will run faster, but my understanding is that it will not find many reads with more than 3 mismatches. Moreover, if your reads are from 454, which is subject to short indel ...
written 6.2 years ago by Bob Harris190

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