User: kspata

gravatar for kspata
kspata40
Reputation:
40
Status:
New User
Location:
Chicago
Last seen:
2 days, 2 hours ago
Joined:
2 years, 2 months ago
Email:
k*****@gmail.com

Posts by kspata

<prev • 81 results • page 1 of 9 • next >
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Error running samjdk.jar for extracting reads containing indels
... Hi All, I want to extract all reads containing a variant from a co-ordinate sorted bam file. The variant is an 11 bp long insertion starting at base position 39. I am running `samjdk.jar` script as per instructions in the post here: https://www.biostars.org/p/283969/ I modified the input file Scr ...
samjdk jvarkit alignment indels written 17 days ago by kspata40
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Comment: C: Effect of trimming on alignment and fastqc report.
... Thank you for explanation. I have learned a lot through this post !!! ...
written 22 days ago by kspata40
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Comment: C: Effect of trimming on alignment and fastqc report.
... Thank you!! Changing the parameter to `--very-sensitive-local` did not alter the variant call result. I also tried `end_to_end` but that also gave the variant at same frequency. I appreciate the help. I am beginning to understand how the alignment algorithms work more. ...
written 22 days ago by kspata40
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Comment: C: Effect of trimming on alignment and fastqc report.
... I first performed trimming with trim galore trim_galore -q 30 --length 200 -a AGATCGGAAGAGC --no_report_file --paired Sample.R1.fastq.gz Sample.R2.fastq.gz 2> Sample.trim_galore.err Then I trimmed these reads using the following command for trimmed.R1.fq and trimmed.R2.fq awk '{un ...
written 23 days ago by kspata40
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Comment: C: Effect of trimming on alignment and fastqc report.
... Hi Genomax, I checked again to confirm only reads with bases having Quality greater than 30 were selected. So I am confused about the fastqc results as well. I understand trimming is severe but less stringent trimming is leading to a false variant call at much higher frequency. Can you please ref ...
written 23 days ago by kspata40
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Effect of trimming on alignment and fastqc report.
... Hi All, I have MiSeq PE250 reads for a viral vector sample. I trimmed the raw reads with Trim Galore (length >= 200 and Q >= 30). I aligned these reads using both `BWA MEM` and `Bowtie2 --local` and found a `AAA -> TTT` variant in both alignment files at different frequencies `9%` and `71% ...
alignment trim galore next gen fastqc written 23 days ago by kspata40 • updated 23 days ago by Friederike3.8k
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Comment: C: Partially map reads to a reference genome
... Thank you!!! I will try this out. ...
written 7 weeks ago by kspata40
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Comment: C: Partially map reads to a reference genome
... How can I obtain these reads which are partially aligned. Will this information be available in the SAM file? I am using bowtie2 as aligner. ...
written 7 weeks ago by kspata40
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Comment: C: Partially map reads to a reference genome
... I am looking to obtain sequence of a gene into which vector DNA is inserted. I do not have the genome reference and only have the plasmid reference. ...
written 7 weeks ago by kspata40
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Partially map reads to a reference genome
... Hi, I have genomic DNA samples sequenced on MiSeq PE 150. I have trimmed these raw reads with Trim_galore and the length distribution of the trimmed reads is now from 50bp - 150bp. Is there a way that I can partially map the reads to a reference sequence. For example, break a read into fragments of ...
binning alignment sequencing written 7 weeks ago by kspata40

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Popular Question 7 days ago, created a question with more than 1,000 views. For Convert blastn to gff3
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Convert blastn to gff3

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