User: mark.rose

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mark.rose20
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United States
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1 month, 1 week ago
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m********@syngenta.com

Posts by mark.rose

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Comment: C: Picard ExtractIlluminaBarcodes error
... IlluminaBasecallsToSam skips the formation of fastqs and goes directly to unaligned BAM files. These BAM files contain a tag (RX) for each read that specifies the associated UMI. From here (presuming I can find a way past here) its on to Picard's SamToFastq to generate fastqs. These fastqs contai ...
written 3 months ago by mark.rose20
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Comment: C: Picard ExtractIlluminaBarcodes error
... I was able to check with them and they confirmed this was the intended structure (they use it for QC runs. I was under the impression that this was the actual production run and that is why my specified read structure was what itoriginally was and wrong) I'm presuming your reformat.sh comment was ...
written 3 months ago by mark.rose20
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Comment: C: Picard ExtractIlluminaBarcodes error
... Perhaps, but it appears to be correct in that: 1) it is written here by the sequencer during the run; and 2) I no longer get an error when running ExtractIlluminaBarcodes and the results produced are sane. That said I am getting an error when trying to execute the next step in the prescribed proces ...
written 3 months ago by mark.rose20
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Answer: A: Picard ExtractIlluminaBarcodes error
... OK, I have discovered the cause of this problem. I did not have the right information about the length of the reads in this run and so my READ_STRUCTURE was wrong. If anyone encounters this error, refer to the file RunInfo.xml in the base directory of the sequencing run to make sure you have the ...
written 3 months ago by mark.rose20 • updated 3 months ago by genomax55k
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Comment: C: Picard ExtractIlluminaBarcodes error
... Yes, it is tab-delimited. And I have tried a few different versions of it as well with no success, including only using 3 columns when trying to demultiplex based on a single index and reordering the columns to "barcode_name library_name barcode_sequence_1 barcode_sequence_2" as suggeste ...
written 3 months ago by mark.rose20
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Comment: C: Picard ExtractIlluminaBarcodes error
... I was originally looking at UMI-tool but then switched to the picard/fgbio approach as it is what is recommended by IDT, the supplier of the unique, dual index, UMI adapters that are being used in this study. If I can't get this approach to work, I will further explore your suggestions. Thanks ...
written 3 months ago by mark.rose20
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Picard ExtractIlluminaBarcodes error
... Hello I tried posting this question to the Broad's GATK help forum, as suggested in the picard documentation, but haven't yet gotten a response so I'm posting it here to the good people of Biostars. I'm using ExtractIlluminaBarcodes (picard version 2.18.7) for the first time and am encountering a ...
picard extractilluminabarcodes demultiplex written 3 months ago by mark.rose20
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Comment: C: IGV SNP glyph question
... Not sure of your point. Yes, I am viewing them here as pairs. When I view them singly, they are solid bars, where the blue ones (in this case) are present only in one of the two overlapping reads. For other SNPs (viewed as pairs, not shown) that occur in overlapping regions but are called in both ...
written 4 months ago by mark.rose20
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Comment: C: IGV SNP glyph question
... Note the darker arrowhead of read 2's overlap at position 15 ...
written 4 months ago by mark.rose20
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Comment: C: IGV SNP glyph question
... Dont know why its not visible in the post but if you right click either of these links the you can open the image Ah, wait. Now its visible ...
written 4 months ago by mark.rose20

Latest awards to mark.rose

Popular Question 12 weeks ago, created a question with more than 1,000 views. For calling phased variants
Scholar 3 months ago, created an answer that has been accepted. For A: Picard ExtractIlluminaBarcodes error
Popular Question 14 months ago, created a question with more than 1,000 views. For freebayes haplotype calling (phased variants)
Popular Question 14 months ago, created a question with more than 1,000 views. For discordant alignments when bowtie2 set to --no-discordant
Popular Question 3.6 years ago, created a question with more than 1,000 views. For unexpected bowtie2 unpaired alignment behavior

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