Moderator: Charles Warden

gravatar for Charles Warden
Charles Warden7.2k
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Duarte, CA
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@cwarden45
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I am a Bioinformatics Specialist at City of Hope, where I work in the Integrative Genomics Core doing microarray and high-throughput sequencing analysis.

However, the feedback that I provide represent my own personal opinions.

Posts by Charles Warden

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Comment: C: Calling Single-Barcode Samples from Mixed Runs as Dual-Barcode Samples | Possibl
... To be honest, I don't remember exactly why it was done the first time (I think our manager Jinhui Wang asked me to do something for one run, and then the IGC director Xiwei Wu asked me to check other runs). However, I think I pretty much agree with your concerns. In particular, if we don't get eno ...
written 1 day ago by Charles Warden7.2k
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Comment: C: Calling Single-Barcode Samples from Mixed Runs as Dual-Barcode Samples | Possibl
... Also, even if you aren't a sequencing facility (and may therefore not have access to your index reads), you can get a sense of index mismatches and/or barcode hopping if you have a small fragment size. For example, if you are feeling ambitious, you could take a look at some of the code that I wrote ...
written 1 day ago by Charles Warden7.2k
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Comment: C: Calling Single-Barcode Samples from Mixed Runs as Dual-Barcode Samples | Possibl
... Thank you for the feedback. **I also hadn't though about changing where you allow 1 mismatch (when starting with dual-barcode samples).** That was a good idea. A loss of 5-15% of reads is a better problem than 5-15% of cross-contamination of reads (however, with the exception of the PhiX example ...
written 1 day ago by Charles Warden7.2k
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Comment: C: Calling Single-Barcode Samples from Mixed Runs as Dual-Barcode Samples | Possibl
... No problem. That newer HiSeq 2500 is currently at 600+ runs. While I'm not sure exactly what to say, at least this means there is at least one other facility that it sounds like has similar use of their machine. Thank you very much for the prompt feedback! ...
written 12 days ago by Charles Warden7.2k
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Comment: C: Calling Single-Barcode Samples from Mixed Runs as Dual-Barcode Samples | Possibl
... ***Update (8/12/2019)***: There was something that I misunderstood about the 2 HiSeq 2500 sequencers, which I am updating here. While there are physically 2 HiSeq 2500 sequencers in the building, all the runs in this post are from the newer sequencer. The first sequencer was originally a HiSeq 200 ...
written 12 days ago by Charles Warden7.2k
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Comment: C: RepBase alternative for maker?
... That is strange. I am already registered, but RepBase was free for me to use. Given that I only have one non-profit e-mail address, I can't really do a perfect test at this point. However, I tested creating an account with my Gmail address. At the first step, the registration said that it was su ...
written 12 days ago by Charles Warden7.2k
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Comment: C: Calling Single-Barcode Samples from Mixed Runs as Dual-Barcode Samples | Possibl
... **Update (8/9)**: At least for this sequence, it looks like BLAST now gives PhiX as the top hit (instead of 16S). However, I think the underlying problem (the need to remove / re-annotate **all** of the sequences for a particular study) is still true. For example, today, this other random PhiX seq ...
written 15 days ago by Charles Warden7.2k
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Answer: A: RepBase alternative for maker?
... I'm not sure what matters most for your specific project. In general, I guess the issue that that you are working for a commercial company? Otherwise, as mentioned above, the registration should be free for non-profits (but I don't remember exactly how long it look to create an account): https:// ...
written 15 days ago by Charles Warden7.2k
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Comment: C: maker has been running for a long time
... I am surprised that you weren't approved - perhaps there is just a general delay in the response time? Maybe you can contact the corresponding author to see if there is some issue with the approval system? It's been a little while (although some of that content is in their archive). At first, I t ...
written 18 days ago by Charles Warden7.2k
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Comment: C: maker has been running for a long time
... Hmm - the website does say approval is required after sending a message to *maker-devel@yandell-lab.org*. However, in the meantime, you can see all the other responses, if that is helpful (and, hopefully, you will be approved soon). ...
written 19 days ago by Charles Warden7.2k

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Scholar 18 days ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 5 weeks ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
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Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 11 weeks ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 5 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 5 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 6 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 6 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 7 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Student 8 months ago, asked a question with at least 3 up-votes. For Mutations Not Recognized in MuSiC
Scholar 9 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 9 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 10 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 11 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim
Scholar 11 months ago, created an answer that has been accepted. For A: Is it good idea to use two different quatification methods from TCGA at same tim

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