Hi,
I would like to search an entry from the SRA and extract the average lengths of each paired read. I've spent the evening trying to bend ncbi eutils to my will. However, I cannot seem to get the right options for the xtract command. I have tried different combinations of -pattern, -element, -group and -block but to no avail.
The start of my command is esearch -db sra -query SRR350075 | efetch. The average lengths in this instance are "120". Here's the XML line: <"Read index="1" count="34203394" average="120" stdev="0""> (I'm not sure how to escape the <> for this message.).
I would greatly appreciate some help and the explanation. I can extract certain information from the XML but not others.
Many thanks
James
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written
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JamesW •
1 answer
esearch -db sra -query SRR350075 | efetch -format xml | xtract -pattern 'RUN' -element Read@average
120
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