User: varsha619

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varsha61970
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Posts by varsha619

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Comment: C: STAR for chip-seq
... Ah I see, thank you! ...
written 11 weeks ago by varsha61970
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Comment: C: STAR for chip-seq
... I will check this, thank you for your help! ...
written 11 weeks 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 weeks 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 weeks 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 weeks ago by varsha61970
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Comment: C: STAR for chip-seq
... @genomax, The average read size is 50-75bp ...
written 11 weeks ago by varsha61970
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STAR for chip-seq
... Hello, Is STAR aligner recommended for use with ChIP-seq data? I am trying to use STAR for ChIP-seq data to obtain reads mapped to multiple regions of the genome with mismatch options, which STAR seems to do better than Bowtie2. I get only around 14% of reads mapped, and around 80% in "% of re ...
alignment chip-seq star written 12 weeks ago by varsha61970 • updated 12 weeks ago by predeus600
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Comment: C: fasta to bed format with more information that just chr locations
... Thank you! I liked the 2nd method the best and seemed to be the easiest to use - cut -f2,3 -d";" test.txt| cut -d= -f2,3 | awk -v OFS="\t" -F':|=|;|\\..|{' '{print "chr"$1,$2,$3,$5}' ...
written 3 months ago by varsha61970
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Comment: C: fasta to bed format with more information that just chr locations
... @Daniel, would you mind explaining how the columns $5 and $10 are defined, when I run the script it does not output the right values. And yes I would like the output values to be tab separated. Thanks! ...
written 3 months ago by varsha61970
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fasta to bed format with more information that just chr locations
... Hello, I have a fasta file with lines of format - >FBti0019256 type=transposable_element; loc=2L:22300300..22304444; name=invader2{}555; dbxref=FlyBase_Annotation_IDs:TE19256,FlyBase:FBti0019256; MD5=d9259a0e33aad699215e64916bd47a5b; length=4145; release=r6.19; species=Dmel; I would ...
fasta to bed written 3 months ago by varsha61970 • updated 3 months ago by Daniel3.6k

Latest awards to varsha619

Supporter 12 weeks ago, voted at least 25 times.
Popular Question 5 months ago, created a question with more than 1,000 views. For Which ChIP-seq IgG to use?
Popular Question 14 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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