User: mark.rose

gravatar for mark.rose
mark.rose30
Reputation:
30
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New User
Location:
United States
Last seen:
1 week, 5 days ago
Joined:
4 years, 6 months ago
Email:
m********@syngenta.com

Posts by mark.rose

<prev • 71 results • page 1 of 8 • next >
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BBMAP fails to find secondary alignment
... I am using BBMAP to align to a reference genome. I am allowing secondary hits because it is my intention to evaluate the mapping quality of those hits to identify and discard query sequences that produce multiple hits with MAPQs above a certain threshold compared to the top hit (i.e. I only want to ...
bbmap secondary written 3 months ago by mark.rose30 • updated 12 weeks ago by Biostar ♦♦ 20
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Comment: C: BBMAP paired end alignment problem
... Hey, thanks for the tip ...
written 3 months ago by mark.rose30
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Comment: C: BBMAP paired end alignment problem
... Yes, it occurred to me ( in the middle of the night ;-) ) that I should check the bitflags. Thanks for taking a closer look too. I will keep this in mind. ...
written 3 months ago by mark.rose30
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Comment: C: BBMAP paired end alignment problem
... $ samtools view SMX008C05-00067_S67_L001.aligned.sam | head -5 K00333:82:HTWHKBBXX:1:1101:27844:3565 1:N:0:TGCAACCGGTCC 99 MAIZE_B73_REF_5_GENOME|10 41935338 10 3=1X3=3X3=2X2=3X1=6X1=1X1=1X2=2I1X3=2X2=2X7=1X1=1X1=53D2=2X4=1X85= = 41935473 285 ...
written 3 months ago by mark.rose30
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BBMAP paired end alignment problem
... I'm aligning 150bp paired end Illumina data to a reference with bbmap ~/BioInfo/bin/BBMap_38.06/bbmap/bbmap.sh \ pairedonly=t \ ambiguous=toss \ killbadpairs=t \ pairlen=1000 \ ...
paired-end bbmap align written 3 months ago by mark.rose30 • updated 3 months ago by h.mon23k
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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 8 months ago by mark.rose30
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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 8 months ago by mark.rose30
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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 8 months ago by mark.rose30
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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 8 months ago by mark.rose30 • updated 8 months ago by genomax62k
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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 8 months ago by mark.rose30

Latest awards to mark.rose

Popular Question 3 months ago, created a question with more than 1,000 views. For Varscan variant calll error on pacbio data
Popular Question 3 months ago, created a question with more than 1,000 views. For bam- readcount error
Popular Question 3 months ago, created a question with more than 1,000 views. For calling phased variants
Popular Question 3 months ago, created a question with more than 1,000 views. For freebayes haplotype calling (phased variants)
Popular Question 7 months ago, created a question with more than 1,000 views. For calling phased variants
Scholar 8 months ago, created an answer that has been accepted. For A: Picard ExtractIlluminaBarcodes error
Popular Question 19 months ago, created a question with more than 1,000 views. For freebayes haplotype calling (phased variants)
Popular Question 19 months ago, created a question with more than 1,000 views. For discordant alignments when bowtie2 set to --no-discordant
Popular Question 4.0 years ago, created a question with more than 1,000 views. For unexpected bowtie2 unpaired alignment behavior

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