User: Ian Fiddes

gravatar for Ian Fiddes
Ian Fiddes70
Reputation:
70
Status:
Trusted
Location:
Santa Cruz
Last seen:
5 months, 2 weeks ago
Joined:
8 years, 8 months ago
Email:
i***********@gmail.com

PhD Candidate, Haussler lab, UC Santa Cruz.

Posts by Ian Fiddes

<prev • 8 results • page 1 of 1 • next >
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Extract linear representation of paths in VG graph
... I am trying to use VG effectively as a genome compression tool for collections of highly related genomes. A key component of this is that I need to be able to randomly access subregions of an input genome, or path. How can this be accomplished with VG? So far, as a test case, I have built a graph o ...
vg written 7 months ago by Ian Fiddes70 • updated 7 months ago by Jouni Sirén90
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Split a BAM within a chromosome without losing read pairs
... I am trying to figure out a way to split up a BAM file into many small pieces without splitting up read pairs. The resulting BAM files needs to be name-sorted, although that operation could be performed on each chunk after the splitting process. As far as I can tell, there aren't any existing tools ...
bam rna-seq written 3.7 years ago by Ian Fiddes70 • updated 3.7 years ago by dariober11k
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Annotating putative novel protein sequences - finding orthologs
... I am working on annotating a few hundred transcripts that may or may not be novel. It is likely that most are orthologs that I was unable to detect via genome alignment, while a couple may be truly novel or have a more distant ortholog. To approach this, I have been running blastp locally against th ...
genome gene sequence written 4.5 years ago by Ian Fiddes70 • updated 4.5 years ago by natasha.sernova3.7k
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Comment: C: Creating custom ALT references for BWA
... I tried producing a FASTA with the format ${chrname}_alt and generating a BWA index. BWA did not recognize the alts. If you look at the bwakit readme, and in particular the file list, he mentions having ALT alignments. There also appears to be an additional index file in ALT indicies. https://gith ...
written 4.6 years ago by Ian Fiddes70
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Creating custom ALT references for BWA
... I am looking for a guide on how to produce custom ALT references for BWA. Maybe I am missing something, but I can't find anything on google. I am working on a segmentally duplicated region of hg38 in which there are haplotypes I have established to be significantly different than the reference. I wa ...
bwa written 4.6 years ago by Ian Fiddes70 • updated 4.6 years ago by abascalfederico1.1k
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Estimated Insert Size Less Than Read Pair Sizes (180Bp For 100X100 Pe), But Seqprep Merged 0 Reads?
... I have some RNAseq that was done by a one-stop shop type company, aka RNA was submitted and then analyzed data as well as fastq files were returned. I am trying to run tophat/cufflinks analysis myself to compare. I used Bowtie Picard tools to empirically determine the insert size (following http://v ...
rna-seq written 8.5 years ago by Ian Fiddes70 • updated 8.2 years ago by Rm8.0k
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Comment: C: Downstream Analysis Of Assembled Transcripts (Cufflinks, Trinity)
... I forgot to check back here, sorry. I got shown the software blast2go on seqanswers, which does what I want, but unfortunately is quite slow and cumbersome. I am currently working on a (crappy) python script to do this for me, for now with Cuffdiff output. My approach is: 1) Take only significant hi ...
written 8.6 years ago by Ian Fiddes70
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Downstream Analysis Of Assembled Transcripts (Cufflinks, Trinity)
... Are there any good available programs/scripts for analyzing assembled transcripts? I imagine something like a script to blastn, blastx and tblastx each transcript and report the best hit. Something like that wouldn't be too hard to write, but I don't want to re-invent the wheel, and I also am concer ...
trinity cufflinks analysis blast written 8.7 years ago by Ian Fiddes70 • updated 8.7 years ago by Rt90

Latest awards to Ian Fiddes

Popular Question 20 months ago, created a question with more than 1,000 views. For Split a BAM within a chromosome without losing read pairs
Appreciated 8.5 years ago, created a post with more than 5 votes. For Downstream Analysis Of Assembled Transcripts (Cufflinks, Trinity)
Popular Question 8.5 years ago, created a question with more than 1,000 views. For Downstream Analysis Of Assembled Transcripts (Cufflinks, Trinity)
Student 8.5 years ago, asked a question with at least 3 up-votes. For Downstream Analysis Of Assembled Transcripts (Cufflinks, Trinity)
Autobiographer 8.5 years ago, has more than 80 characters in the information field of the user's profile.

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