User: varsha619

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varsha61970
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Posts by varsha619

<prev • 78 results • page 1 of 8 • next >
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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 7 months ago by varsha61970
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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 7 months ago by varsha61970
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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 7 months ago by varsha61970
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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 7 months ago by varsha61970
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Comment: C: STAR for chip-seq
... Ah I see, thank you! ...
written 11 months ago by varsha61970
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Comment: C: STAR for chip-seq
... I will check this, thank you for your help! ...
written 11 months ago by varsha61970
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Comment: C: STAR for chip-seq
... @genomax, does Bowtie2 output unaligned reads by default? Even when I don't use --un option ...
written 11 months ago by varsha61970
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Comment: C: STAR for chip-seq
... STAR --genomeDir /genomes/dm6/Sequence/STARindex --runThreadN 8 --readFilesIn in.fastq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix star_out ...
written 11 months ago by varsha61970
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Comment: C: STAR for chip-seq
... Bowtie2 also gave me only 18% alignment but I was confused because the file sizes are not comparable. The bam file from Bowtie2 (1,035,494,925) is much larger than the one from STAR (275,497,682). P.S. It's fly genome, hence the smaller sizes. ...
written 11 months ago by varsha61970
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Comment: C: STAR for chip-seq
... @genomax, The average read size is 50-75bp ...
written 11 months ago by varsha61970

Latest awards to varsha619

Popular Question 6 months ago, created a question with more than 1,000 views. For bedGraphToBigWig error - end coordinate bigger than chr
Popular Question 6 months ago, created a question with more than 1,000 views. For Which ChIP-seq IgG to use?
Supporter 12 months ago, voted at least 25 times.
Popular Question 14 months ago, created a question with more than 1,000 views. For Which ChIP-seq IgG to use?
Popular Question 23 months 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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