Moderator: cpad0112

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cpad011211k
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Posts by cpad0112

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Comment: C: Bam header editing
... you can use picard replace sam header. https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.0.0/picard_sam_ReplaceSamHeader.php ...
written 1 day ago by cpad011211k
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Comment: C: Extract in specific column with patter file
... $ awk 'FNR==NR {a[$0]++; next} {if ($2 in a) print $0}' file1.txt file2.txt ...
written 3 days ago by cpad011211k
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Comment: C: Extract in specific column with patter file
... output: $ join -1 1 -2 2 <(sort -k1 test1.txt) <(sort -k2 test.txt) -o 2.1,2.2 ST-E00243:601:HWJFHCCXY:8:1101:19512:10468 512 ST-E00243:601:HWJFHCCXY:8:1101:19431:10468 9606 input: $ cat test1.txt 2485233 2485231 2059665 2029516 512 2022430 20224 ...
written 3 days ago by cpad011211k
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Comment: C: Splitting string in a column using character
... sed 's/.*\(rs\w\+\).*/\1/g' test.txt Col1 rs10136766 rs104894363 rs10774624 rs111647200 rs117306900 rs117306950 rs117306954 rs117306975 rs117306989 rs532891158 rs794728599 rs121913344 rs12979860 rs397518008 rs397518039 rs6837175 ...
written 4 days ago by cpad011211k
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Comment: C: Splitting string in a column using character
... $grep -Po '(?<=^|-)rs\w*' test.txt rs10136766 rs104894363 rs10774624 rs111647200 rs117306900 rs117306950 rs117306954 rs117306975 rs117306989 rs532891158 rs794728599 rs121913344 rs12979860 rs397518008 rs397518039 rs6837175 r ...
written 4 days ago by cpad011211k
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Comment: C: Having trouble using wildcard
... You can check the file existence with following code. Please change the path as per your convenience: for i in {17..34}; do if [ -e ./MBM1${i}_R1_001.fastq ]; then echo "exists";fi;done @ https://www.biostars.org/u/40545/ ...
written 5 days ago by cpad011211k
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Comment: C: Having trouble using wildcard
... I think OP code still has a problem (assuming that it is updated): `in1=./temp_expt/Sample_MBM1${i}/MBM1${i}_R1_001.fastq`.. this would look only for `MBM118_R1_001.fastq` under `sample_MBM118` folder, but not for `MBM18*_R1_001.fastq`. Error should be some thing like this: `Can't find file ./t ...
written 5 days ago by cpad011211k
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Comment: C: Having trouble using wildcard
... well, this is confusing. Your code is supposed to throw a different error. copy/pasted the code from OP: for i in {17..34}; do bash bbmap/bbsplit.sh in1=./temp_expt/Sample_MBM1${i}/MBM${i}_R1_001.fastq in2=./temp_expt/Sample_MBM1${i}/MBM1${i}_R2_001.fastq ref=./MG1655.fasta,./MGH78578.fasta,./ ...
written 5 days ago by cpad011211k
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Comment: C: Differential expression analysis for time course data
... edgeR has a function for CPM calculation from counts ...
written 5 days ago by cpad011211k
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Comment: C: Interesting Bioinformatics Project Ideas (NGS, RNA-Seq)
... This is ad for selling the company/website services. Please tag accordingly. https://www.biostars.org/u/16084/ ...
written 5 days ago by cpad011211k

Latest awards to cpad0112

Commentator 5 days ago, created a comment with at least 3 up-votes. For C: Problem installing Rgraphviz in R
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
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Scholar 5 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
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Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: How to make a clear box plot or whatever beautiful for showing the ratio of two
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Teacher 3 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
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Teacher 3 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
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Teacher 4 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 4 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 4 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 4 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 4 months ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change

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