User: fadhil.abubaker

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Posts by fadhil.abubaker

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Comment: C: intersectBed extremely large read lengths
... My question is why does such a long read exist if STAR says the average read input length is 101? ...
written 3 months ago by fadhil.abubaker20
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intersectBed extremely large read lengths
... I've run intersectBed as follows ``` intersectBed -a introns.bed -b accepted_hits.bam -wao > result.bed ``` Where ```introns.bed``` is a bed file containing all introns in hg38 and ```accepted_hits.bam``` is from STAR. Now, the average read input length as reported by STAR is 101. However whe ...
rna-seq sequencing written 3 months ago by fadhil.abubaker20 • updated 3 months ago by ATpoint8.0k
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Comment: C: Understanding IntersectBed columns
... That definitely makes sense, although I'm a bit confused as to what the 15th column stands for. I understand it comes from the bam file, but I'm not sure what it stands for. ...
written 3 months ago by fadhil.abubaker20
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Understanding IntersectBed columns
... I'm running intersectBed as follows: ``` intersectBed -a introns.bed -b accepted_hits.bam -wao > result.bed ``` Where ```introns.bed``` is a bed file containing all introns in hg38 and ```accepted_hits.bam``` is from STAR. Here is a sample row from ```result.bed```: ```chr1 13220 14409 ...
next-gen rna-seq written 3 months ago by fadhil.abubaker20 • updated 12 weeks ago by Biostar ♦♦ 20
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Comment: C: Obtaining exon-intron and intron-exon reads
... We used STAR to get the alignments. ...
written 4 months ago by fadhil.abubaker20
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Obtaining exon-intron and intron-exon reads
... We're interested in studying the number of reads that start at an exon and "spill" over into the subsequent intron or vice-versa. We have aligned .bam files and annotation files for h38. What tools/software could we use to get the number of reads from the .bam file that span exon-intron / intron- ...
next-gen rna-seq written 4 months ago by fadhil.abubaker20 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: Migrating pipeline from TopHat to STAR
... Is it safe to say that TopHat2's results above are wrong and should not be used for any downstream analysis? Does anyone know of a different program that I can use to extract splice junction information? This way I have a third dataset for compare. ...
written 5 months ago by fadhil.abubaker20
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Comment: C: Migrating pipeline from TopHat to STAR
... I did try two-pass mode with STAR but it barely made any difference. It's just that the discrepancy between the two is so large I'm not actually sure which to trust. ...
written 5 months ago by fadhil.abubaker20
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Migrating pipeline from TopHat to STAR
... Hey all, Our current pipeline for alignment and analysis uses TopHat + Cufflinks and we wish to replace TopHat with STAR. We are in particular interested in splice junctions so we ran STAR against a sample and compared both the junctions file from TopHat and STAR. For some reason, TopHat seems to ...
alignment rna-seq written 5 months ago by fadhil.abubaker20 • updated 5 months ago by RamRS18k
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Comment: C: Low mapping rate for Tophat2
... In the end rebuilding indices helped a bit but I was still getting low mapping rate. Turns out the fastq files were corrupted and re-downloading them helped. Thanks for everyone's help! ...
written 10 months ago by fadhil.abubaker20

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