Hi, I downloaded MCF7 H3K4me1 (ENCFF191EBN) and H3K4me3( ENCFF132IPF) narrow peak file from ENCODE website and I found a portion of peaks are overlap with …

<p>Dear biostars,</p> <p>Does any one have experience using fr-secondstrand versus fr-unstranded library types in tophat. I am running tophat against fr-secondstrand type rna-seq reads but …

<p>Dear Biostars</p> <p>Does some one know where can download mm9 piRNAs in BED or GTF format ?</p> <p>Thanx in advance</p>

<p>Dear biostars, </p> <p>Do you know how one can separate noncoding from coding UCSC and ENSEMBL transcripts ? In general I use NR_* to identify …

<p>Dear biostars,</p> <p>I am wondering what do you do if any author do not share his/her published data with you ? Usually I send an …

<p>Hi, </p> <p>I have 2 very straight forward questions. </p> <ol> <li>What exactly is fastqc "duplicated read" definition (reads having similar sequences ? or reads …

<p>Hi guys, I downloaded hg19 and mm9 repeat masker repeats from UCSC table browser. Do you know how to separate transposon-derived repeats from other repeats …

<p>I have 200 genes and 15 tissue RNA-Seq RPKM units (15 mouse tissues). I can see which tissue has high expression compared to others. But …

<p>Liftover tool can not do this operation. Does any know how to handle this problem ?</p> <p>Thanx</p>

<p>Hi, </p> <p>I know that, I can do this manually by going to either GEO or at once by going to ENCODE: ENCODE certainly does …