User: st.ph.n

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st.ph.n650
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Philadelphia, PA
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Posts by st.ph.n

<prev • 244 results • page 1 of 25 • next >
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Comment: C: Use egrep on only one column
... That's why I included the `sed` line above. ...
written 4 hours ago by st.ph.n650
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Comment: C: Use egrep on only one column
... original input from OP is space delimited, would need to convert to tab. ...
written 5 hours ago by st.ph.n650
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Comment: C: Use egrep on only one column
... Ok, your comment on harold's answer led me to believe you only needed col 1, and the separated field in col 2. ...
written 8 hours ago by st.ph.n650
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Answer: A: Use egrep on only one column
... An issue here is the number of spaces, and not tabs between your columns, and I'm assuming that cols 1,4 represent the information in col 2 separting by `:`. To make this easier, you can convert any number of spaces to tabs with `sed`: sed 's/ \+ /\t/g' infile > tab_sep_file then cut, repla ...
written 8 hours ago by st.ph.n650
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Comment: C: extracting multiple columns from a file
... I think the OP had an excel file, but wanted to use R. ...
written 9 hours ago by st.ph.n650
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Comment: C: extracting multiple columns from a file
... Have you tried anything in R? Since you have an Excel file, I would save as text tab-delimited. egrep 'MYC|YY1|TP53' transmir_v1.2.txt | awk -F'\t' '{if ($6=="human") { print } } > filtered.txt ...
written 1 day ago by st.ph.n650
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Answer: A: Split single columm into multiple colums
... Here's a multi-step process so you can see how it's done: Pull out the chromosome ids from your file cut -f 1 -d '_' infile.txt | sort | uniq > all_chrom_ids.txt Put this into a bash file (`get_ids.sh`): #!/usr/bin/bash grep -e "$1"_ all_chrom_ids.txt > "$1"_snps.txt Use ...
written 1 day ago by st.ph.n650
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Comment: C: awk code question
... I don't know what a narrowPeak file looks like (it would help if you showed an example in your post), but that would print the entire line, where column 8 is greater than 8. I typically use a syntax such as this: awk -F'\t' '{if($8>8) { print } }' infile.txt ...
written 2 days ago by st.ph.n650
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Comment: C: Best de novo genome assemblies using only Illumina data ??
... Please rephrase the post title to reflect more of what you're looking for. ...
written 2 days ago by st.ph.n650
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Answer: C: to pool or not to pool
... It is both preferred, and better. In order to map the raw reads from the different samples, you should pool your samples by read orientation (all R1's, and all R2's) into the assembly. If you're using Trinity, they specifically recommend this: > If you have multiple RNA-Seq data sets that you wa ...
written 6 days ago by st.ph.n650

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