User: varsha619

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varsha61990
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Posts by varsha619

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Comment: C: Bowtie2 hg19 reference for gatk MuTect
... Worked after I created the bowtie2 indices for the GATK bundle hg19 genome file, thank you. ...
written 14 months ago by varsha61990
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Comment: C: Bowtie2 hg19 reference for gatk MuTect
... Yes this fixed the issue, my bad. Thank you! ...
written 14 months ago by varsha61990
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Comment: C: Bowtie2 hg19 reference for gatk MuTect
... Yes both the files have the format chr1, chr2, ... ...
written 14 months ago by varsha61990
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Comment: C: Bowtie2 hg19 reference for gatk MuTect
... I did keep the reference files consistent through the steps. I meant to say that I tried using both files separately. I can successfully align the files using hg19 Bowtie2 indices but then I get a compatibility error in MuTect with dbsnp_138.hg19.vcf file while running GATK MuTect. If I try to use t ...
written 14 months ago by varsha61990
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Comment: C: Bowtie2 hg19 reference for gatk MuTect
... This is the error I get with the fasta file I downlaoded from - ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg19/ bowtie2 -p 4 -x ucsc.hg19.fasta -1 R1_001.fastq.gz -2 R2_001.fastq.gz | samtools view -bS - > 001_out.bam (ERR): "ucsc.hg19.fasta" does not exist or is not a Bowtie 2 ...
written 14 months ago by varsha61990
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Bowtie2 hg19 reference for gatk MuTect
... Hello, I understand that the suggested aligner to use with GATK is bwa. If I want to use Bowtie2 as the aligner, which reference file should I be using? The reference in GATK bundle (Homo_sapiens_assembly19.fasta) does not seem to work with Bowtie2 and using hg19 Bowtie2 index from http://bowtie-bio ...
gatk bowtie2 written 14 months ago by varsha61990 • updated 14 months ago by h.mon31k
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Comment: C: UCSC itemRgb on column 9
... They look fine except for all tracks in black and not color, sorry I am unable to upload a screenshot here. ...
written 24 months ago by varsha61990
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Comment: C: UCSC itemRgb on column 9
... Yes I did follow the steps in the link and my bed file example is as follows (Drosophila genome) - chr2L 7597 7617 4.62708799702989 4.62708799702989 . 7597 7617 255,0,0 chr2L 10912 10932 5 5 . 10912 10932 0,0,255 chr2L 17527 17547 4.76955107862173 4.76955107862173 . 17527 ...
written 24 months ago by varsha61990
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Comment: C: UCSC itemRgb on column 9
... I used Chrom, Start, End columns, column 4 and 5 are the same (scores), column 6 is ".", columns 7 and 8 are the same as columns 2 and 3, and column 9 is Rgb code. I still don't see the colors in my track, my visibility is full and itemRgb on. I am not sure what I am missing here. Thank you for your ...
written 24 months ago by varsha61990
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UCSC itemRgb on column 9
... Hello, I am trying to set colors to my bed track based on column values using itemRgb on option. I have 1st 3 columns in my bed file for chrom, chromStart and chromEnd, 4th column has the values and 5th column has color codes for rgb for example 0,0,255. I converted the bed to bb format and use ...
ucsc itemrgb written 24 months ago by varsha61990

Latest awards to varsha619

Popular Question 13 months ago, created a question with more than 1,000 views. For Visualize smooth ChIP peaks with Homer makeUCSCfile
Popular Question 20 months ago, created a question with more than 1,000 views. For bedGraphToBigWig error - end coordinate bigger than chr
Popular Question 20 months ago, created a question with more than 1,000 views. For MutSigCV output has p-value of 0
Popular Question 20 months ago, created a question with more than 1,000 views. For Which ChIP-seq IgG to use?
Popular Question 20 months ago, created a question with more than 1,000 views. For Remove reads from fastq file
Popular Question 20 months ago, created a question with more than 1,000 views. For Visualize smooth ChIP peaks with Homer makeUCSCfile
Popular Question 23 months ago, created a question with more than 1,000 views. For bedGraphToBigWig error - end coordinate bigger than chr
Popular Question 23 months ago, created a question with more than 1,000 views. For Which ChIP-seq IgG to use?
Supporter 2.3 years ago, voted at least 25 times.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Which ChIP-seq IgG to use?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files

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