User: Illinu

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Illinu80
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Posts by Illinu

<prev • 30 results • page 1 of 3 • next >
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Answer: A: emtpy bcf file
... This was corrected at the mpileup step with -A option samtools mpileup -ug -A -f thal.fasta $bname-thal.nodup.sorted.bam > $bname-thal.bcf -A, --count-orphans Do not skip anomalous read pairs in variant calling. Maybe this is because the sequences I used as reference are short and the p ...
written 8 weeks ago by Illinu80
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Comment: C: emtpy bcf file
... Thanks @Pierre, I normally run the pipeline for some commands, some of those intermediate files I need for other tasks. But in the script above I am testing this way to see at what step it fails. So far up to the *.nodup.sorted.bam it works well, that's how I know that it is the bcf file that is not ...
written 9 weeks ago by Illinu80
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Comment: C: comparing three genomes?
... and what is the difference for you? It still consists of fasta files with sequences right? The question is how do you do it for three sets of 'genes' (if you want) instead of two. The problem is that what you propose doesn't work when the gene names are not the same, and when there is gene expansion ...
written 9 weeks ago by Illinu80
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emtpy bcf file
... I am aligning genomic reads to a set of 6 genes all saved in one file in fasta format. The sam and bam files look ok but the mpileup step returns empty bcf files, with only the header until: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1-thal.nodup.sorted.bam Th ...
alignment samtools mpileup written 9 weeks ago by Illinu80
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Comment: C: Venndiagram Using R
... Hi Ly, but with this method you cannot see up and down regulated genes right? You just plot significantly differentially expressed ...
written 10 weeks ago by Illinu80
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Comment: C: comparing three genomes?
... I don't see this for a set of three transcriptomes, it only presents option for comparing two nucleotide databases, can you explain how you do this if you have three databases? Thank you ...
written 11 weeks ago by Illinu80
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Comment: C: vcf-consensus Error: Fasta sequence does not match REF
... Hi microfuge, I am getting the same error and I mapping reads from several genotypes to one heterozygous reference and was hoping to get the consensus files for each genotype. Does this error mean it is not possible to get the consensus for each genotype individually? ...
written 4 months ago by Illinu80
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Comment: C: create a gene2accession file from a 2 column file
... Thanks a million @EagleEye, I asked in stackoverflow and my question was blocked because it was '*unclear*' what I was asking for. Note that to get rid of the last occurrence of '|' I used sed 's/BACK_SLASH(.*\)|/\1/'. Thanks again ...
written 10 months ago by Illinu80
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create a gene2accession file from a 2 column file
... I need to create a gene2accession file where one gene ID might have one or more Uniprot entries. My file looks like this: comp100002_c0 Q9FFI3 comp100004_c0 B9DHK3 comp100004_c0 F4J3J5 comp100005_c0 P54150 and I need it to look like this: comp100002_c0 Q9FFI3 c ...
cluego gene2accession go enrichment uniprot written 10 months ago by Illinu80 • updated 10 months ago by EagleEye3.5k
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Answer: A: grep unexpected behaviour
... Just to update, this form: for f in $(cat list.OE.txt); do grep -w $f Trinity_uniref_2015_02_filt_ann_out.txt; done > OE.annocript.txt works A LOT faster than this one: grep -wf list.OE.txt Trinity_uniref_2015_02_filt_ann_out.txt > OE.annocript.txt ...
written 2.1 years ago by Illinu80

Latest awards to Illinu

Epic Question 10 months ago, created a question with more than 10,000 views. For filter out multiple rows based on values in columns - perl and R attempt
Great Question 22 months ago, created a question with more than 5,000 views. For filter out multiple rows based on values in columns - perl and R attempt
Popular Question 22 months ago, created a question with more than 1,000 views. For Python: count how many lines have a specific word
Popular Question 22 months ago, created a question with more than 1,000 views. For filter out multiple rows based on values in columns - perl and R attempt

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