User: Lila M

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Lila M 390
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390
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UK
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18 hours ago
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3 years, 1 month ago
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Posts by Lila M

<prev • 263 results • page 1 of 27 • next >
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Comment: C: how can I get the coverage over introns only in a RNA-seq experiment?
... both , coverage plot and number of reads mapping to INTRONS will be nice :) ...
written 3 days ago by Lila M 390
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how can I get the coverage over introns only in a RNA-seq experiment?
... Hi everybody, I've just wondering the best way to get the coverage over introns (only) in RNA-seq experiments (human genome) My first approach is to download the complete intron list from UCSC. Then I could get the overlaps (using bedtools intersect or samithing similar) with each bed file. Once I ...
introns coverage rna-seq written 4 days ago by Lila M 390
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Comment: C: Problems running VC GATK: SAM/BAM/CRAM file dedup.bam is malformed
... And how can I get this info? ...
written 7 weeks ago by Lila M 390
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Comment: C: Problems running VC GATK: SAM/BAM/CRAM file dedup.bam is malformed
... Not at all with samtools view -H file.bam @HD VN:1.4 SO:coordinate @SQ SN:chr1 LN:248956422 @SQ SN:chr2 LN:242193529 @SQ SN:chr3 LN:198295559 @SQ SN:chr4 LN:190214555 but nothing comes up with: samtools view -H file.bam | grep '^@RG' does it means that my BAM file do ...
written 7 weeks ago by Lila M 390
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Problems running variant calling (VC) GATK: SAM/BAM/CRAM file dedup.bam is malformed
... Hi everybody, I'm trying to carry out some VC analysis, but I'm not very advanced at it, so I am a bit struggle... For my RNA-seq samples, I've run the following command lines: #1 Mark duplicates ls *bam | xargs -I {} -n 1 java -jar picard.jar MarkDuplicates I={} O={}.dedup M={}.metrix.t ...
gatk vc rna-seq written 7 weeks ago by Lila M 390
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Comment: C: How can I get only the rows when for the converge points : - +
... Thank you! I've never heard about this toturial before. ...
written 10 weeks ago by Lila M 390
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Comment: C: How can I get only the rows when for the converge points : - +
... thank you for the update! ...
written 10 weeks ago by Lila M 390
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Comment: C: How can I get only the rows when for the converge points : - +
... Do you know any tutorial or useful documentation to learn awk? I know that should be a separate question but I hope could be permitted ...
written 10 weeks ago by Lila M 390
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Comment: C: How can I get only the rows when for the converge points : - +
... It works as expected, thank you very much. `awk` is very very helpful to solve this kinds of problems, but for me takes a while to learn it... ...
written 10 weeks ago by Lila M 390
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How can I get only the rows when for the converge points : - +
... Hi everybody, Maybe this is more a programming question related, but any advice could be very handy. I'm trying to select the rows when the 4th has convergence points ( **-** following by **+**) in this data sets: chr1 1275000 1284999 + chr1 1285000 1294999 - chr1 1295000 1304999 - ...
R convergence points written 10 weeks ago by Lila M 390 • updated 10 weeks ago by Alex Reynolds26k

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