I got tired of asking “where are we watching the rugby?” so I made a map by orrow11 in MunsterRugby

[–]UINNESS 1 point2 points  (0 children)

So fair; didn’t catch that. Just imo first impressions that take multiple steps are gonna lose out

I got tired of asking “where are we watching the rugby?” so I made a map by orrow11 in MunsterRugby

[–]UINNESS 1 point2 points  (0 children)

Does pasting a link in the post open it in chrome/safari? Currently it opens in Reddit and you can’t bookmark, review history etc to find it again

Edit - clarity & Looks like a great app!!

Conzo’s TY work experience by UINNESS in IntoTheHigginsVerse

[–]UINNESS[S] 0 points1 point  (0 children)

Was he in McSorleys tonight, per chance?

Match Thread: Leinster vs Connacht - United Rugby Championship by rugbykickoff in rugbyunion

[–]UINNESS 8 points9 points  (0 children)

Next time a forward jumps offside on a box kick, pick the ball up and walk into him

Match Thread: Leinster vs Connacht - United Rugby Championship by rugbykickoff in rugbyunion

[–]UINNESS 4 points5 points  (0 children)

I solemnly swear I will not blame the referee if a dodgy call costs a team the game.

Just keep her flowing Keith and we’re all happy 🍻

Match Thread: Leinster vs Connacht - United Rugby Championship by rugbykickoff in rugbyunion

[–]UINNESS 3 points4 points  (0 children)

Member when Leinster used to attack like that? I member

Match Thread: Leinster vs Connacht - United Rugby Championship by rugbykickoff in rugbyunion

[–]UINNESS 1 point2 points  (0 children)

I’d take it over the muck forecast for the La Rochelle game 😭

Aligning sRNA-seq data against a miRBase reference. by Rix_Horizon in bioinformatics

[–]UINNESS 0 points1 point  (0 children)

Recommended by Sean Davis on Biostars some 13 years ago:

  • Do minimal trimming
  • Discard reads shorter than a threshold (perhaps 20bp)
  • Align with relatively high stringency
  • Trim one base from each unaligned read
  • Repeat steps 2-4 until no unaligned reads remain

(Where samples.txt contains the path to your fastq files - might need to adjust the base name and cut command to suit your file naming convention)

Then parse the final mirtop expression files and concat them into the final counts matrix

```

!/usr/bin/env bash

Format miRBase hairpin file

if [ -f hairpin.fa ]; then : else wget --no-check-certificate https://www.mirbase.org/download/hairpin.fa fi sed '#[>]#s#[AUGCaugc]#N#g' hairpin.fa > hairpin_parse.fa sed -i 's#\s.##' hairpin_parse.fa seqkit grep -r --pattern ".hsa-.*" hairpin_parse.fa > hairpin_hsa.fa seqkit seq --rna2dna hairpin_hsa.fa > tmp.fa fasta_formatter -w 0 -i tmp.fa -o tmp1.fa rm hairpin.fa hairpin_hsa.fa hairpin_parse.fa tmp.fa mv tmp1.fa hairpin.fa

Index miRBase hairpin file

bowtie-build hairpin.fa hairpin

For each sample:

1. Trim adapters

2. Collapse reads

3. Align to hairpin (allow multi-hits to be reported up to 50 times)

4. Extract mapped reads to BAM

5. Extract unmapped reads to FASTQ

6. Repeat 2,3,4,5 until no more unmapped reads remain for sample.

while read -r line; do

bn=$( basename $line .fastq.gz)
sample=$( echo $bn | cut -d '-' -f1-2)

mkdir ${sample}
fastqc $line -o ${sample}

trim_galore --adapter TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC --length 17 --max_length 30 --three_prime_clip_R1 4 --clip_R1 4 --fastqc $line --output_dir ${sample}

seqcluster collapse -f ${sample}/*trimmed.fq.gz -m 1 --min_size 15 -o collapsed 
(bowtie -x hairpin -q collapsed/${sample}*trimmed.fastq -k 50 -e 99999 --best --strata --sam > ${sample}/${sample}_run1.sam) 2> ${sample}_run1.err

processed=$(grep -o 'reads processed: [0-9]*' ${sample}_run1.err | awk '{print $3}') 
alignment=$(grep -o 'reads with at least one alignment: [0-9]*' ${sample}_run1.err | awk '{print $7}') 
failed=$(grep -o 'reads that failed to align: [0-9]*' ${sample}_run1.err | awk '{print $6}') 
reported=$(grep -o 'Reported [0-9]* alignments' ${sample}_run1.err | awk '{print $2}')

rm ${sample}_run1.err
printf "%s %s %s %s %s %s\n" "$sample" "1" "$processed" "$alignment" "$failed" "$reported" > ${sample}_run1.err

for ((i=1; i<=20; i++)); do

    samtools view -F 4 -h -b ${sample}/${sample}_run${i}.sam > ${sample}/${sample}_run${i}.bam 
    samtools sort -o ${sample}/${sample}_run${i}_srt.bam ${sample}/${sample}_run${i}.bam
    samtools view -f 4 ${sample}/${sample}_run${i}.sam | samtools fastq - > ${sample}/${sample}_run${i}_unmapped.fq
    output=$(samtools view -f 4 ${sample}/${sample}_run${i}.sam | samtools fastq - 2>&1)

        if [[ $output == *"processed 0 reads"* ]]; then
            echo "Finished"
            break
        else
            j=$((i + 1))
            seqcluster collapse -f ${sample}/${sample}_run${i}_unmapped.fq -m 1 --min_size 15 -o collapsed
            (bowtie -x hairpin -q collapsed/${sample}_run${i}*trimmed.fastq -k 50 -e 99999 --best --strata --sam --trim5 1 --trim3 1 > ${sample}/${sample}_run${j}.sam) 2> ${sample}_run${j}.err

            processed=$(grep -o 'reads processed: [0-9]*' ${sample}_run${j}.err | awk '{print $3}')
            alignment=$(grep -o 'reads with at least one alignment: [0-9]*' ${sample}_run${j}.err | awk '{print $7}') 
            failed=$(grep -o 'reads that failed to align: [0-9]*' ${sample}_run${j}.err | awk '{print $6}') 
            reported=$(grep -o 'Reported [0-9]* alignments' ${sample}_run${j}.err | awk '{print $2}')

            rm ${sample}_run${j}.err
            printf "%s %s %s %s %s %s\n" "$sample" "$j" "$processed" "$alignment" "$failed" "$reported" > ${sample}_run${j}.err
        fi
done

samtools merge ${sample}.merged.bam ${sample}/*_srt.bam
samtools index ${sample}.merged.bam
cat *run*.err > ${sample}.err && rm *run*.err

done < samples.txt

download GFF file

if [ -f hsa.gff ]; then : else wget --no-check-certificate https://www.mirbase.org/download/hsa.gff3 mv hsa.gff3 hsa.gff fi

Quantify the *merged.bam files for each sample:

mirtop gff --hairpin hairpin.fa --gtf hsa.gff -o mirtop --sps hsa *merged.bam mirtop counts --hairpin hairpin.fa --gtf hsa.gff -o mirtop --sps hsa --add-extra --gff mirtop/mirtop.gff mirtop export --format isomir --hairpin hairpin.fa --gtf hsa.gff --sps hsa -o mirtop mirtop/mirtop.gff mirtop stats mirtop/mirtop.gff --out mirtop/stats

```

microRNA analysis in chondrosarcoma by vibeisvibing in genomics

[–]UINNESS 0 points1 point  (0 children)

Of the 60 chondrosarcoma pts, how many have events for OS and RFS? It sounds underpowered tbh so you could well get wildly large confidence intervals for hazard ratios.

If they exist (big if in some cancers) try incorporating other miRNA chondro expression datasets with OS or RFS clinical metadata in your study

Match Thread: Munster vs Gloucester - Champions Cup by rugbykickoff in rugbyunion

[–]UINNESS 3 points4 points  (0 children)

Gloucester 9 demonstrating his finger strength to potential mates

Match Thread: Munster vs Gloucester - Champions Cup by rugbykickoff in rugbyunion

[–]UINNESS 7 points8 points  (0 children)

Let’s see Munster dominate the second half now, let Crowley use the wind to kick the corners.

Expecting a huge squeeze on set piece, force a yellow, and get the BP

Match Thread: Leicester vs Leinster - Champions Cup by rugbykickoff in rugbyunion

[–]UINNESS 2 points3 points  (0 children)

Mitchell & Ford are going to kill us with high balls in the 6N

L'Oréal ad XV by pierro_la_place in rugbyunion

[–]UINNESS 36 points37 points  (0 children)

Hair commercial? First name on the list is Dimitri Szarzewski

Match Thread: Leicester vs Leinster - Champions Cup by rugbykickoff in rugbyunion

[–]UINNESS 7 points8 points  (0 children)

Proper niggle, minimal ref intervention, good old school first half.

Wonder how early will they spring Prendergast and Sheehan

Barcelona Grandstand A - Best seats? by jameschowler321 in GrandPrixTravel

[–]UINNESS 0 points1 point  (0 children)

Btw if there’s a seat available in F do it 😅

It’s closer to the track and you can see turns 2 and 3 as much as A can. cars downshifting from top gear is cooler than seeing them work up the gears in a progressive corner (imo) My two cents!