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血泪求助：Trinity的normalize 已有2人参与
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鄙人最近用Trinity软件normalize一个trim后的数据，奈何一直报错如下： Error, pairs.K25.stats is empty. Be sure to check your fastq reads and ensure that the read names are identical except for the /1 or /2 designation. at /diag/home/aubzyy/trinityrnaseq_r20140717/util/insilico_read_normalization.pl line 865. 这是咋回事啊，俺是新手，跪求大侠出手相助！ 我的数据是Pair-end。。。   |
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2楼2015-01-15 10:29:15
wizardfan
至尊木虫 (著名写手)
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小木虫: 金币+0.5, 给个红包，谢谢回帖
小木虫: 金币+0.5, 给个红包，谢谢回帖
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it says that the name of sequences in your fastq can not match In fastq format, Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line). e.g. @HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/1 another entry would be something like @HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/2 |
3楼2015-01-16 08:09:27
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Thank you. But my sequence starts like this: @SRR1559285.21 HWI-ST531R:238:C346VACXX:5:1101:1193:2038 length=101 CCTTCATTCATGTGCTCACGCCAGTATGCAGCATTTTTAACAGCACAGTCCCAGT +SRR1559285.21 HWI-ST531R:238:C346VACXX:5:1101:1193:2038 length=101 @CCFFFFFGHHGHIIJJJ4FHIJJGIIJJIIJIJJJJJHIJJJIIJJJHHJJJJI @SRR1559285.22 HWI-ST531R:238:C346VACXX:5:1101:1126:2077 length=101 CCTATTCATTTACAGCAGAAGTGCTATTTCTTATTCATGATGTACAAGTCGTTGTTCCGTGAAAATGAAACAGAGACGGG CGTCGTAGGATCCTTAGACGG +SRR1559285.22 HWI-ST531R:238:C346VACXX:5:1101:1126:2077 length=101 CCCFFFFFHHGHHFIJJJHIIIHIJJJIJIJJIHJGGIFHIIGGIIJJFGHGEGHGIGGDGGGJJIIJGHIIIHJJHHHF FD?BDBBBDCCCDDDDC:@@B @SRR1559285.23 HWI-ST531R:238:C346VACXX:5:1101:1228:2083 length=101 CAGACGAATTATAGAAAGGCTGTTTAATTAGAAATTTACTTAATCCAAGTTTTGGCTGAAATGGATTGAAGTTTGTCCTG GAATGTTTCGAACACATCTGT +SRR1559285.23 HWI-ST531R:238:C346VACXX:5:1101:1228:2083 length=101 CCCFFFFFHFHGFIBHIJIJJJJGIGAHIEIHIHHIHIFIIIIIJJJEHHGIJIIHIIGJGIII@FHJGIGCAHEEHHFF FFFCEEEECDDDBDDDDCD:@ @SRR1559285.24 HWI-ST531R:238:C346VACXX:5:1101:1246:2099 length=101 TGAAACTGAGGAATGTATGCCTCTCACGGTGACCCTGTCTCACCGTCTGAACCAAAAAATTGCTGAGCTTCGTAGAGATG GTACATTCTGGTGGGCAAGAC +SRR1559285.24 HWI-ST531R:238:C346VACXX:5:1101:1246:2099 length=101 @@@DF;DDBFFFFGGGHIJJAHGHIGEHGACGIJFIGIIGGIJJJHGIJIIJJEIIIIGGCACEEEFDEFFFDEC;@CCC D@DCDFDDEEDCDDDB?@B<9 @SRR1559285.25 HWI-ST531R:238:C346VACXX:5:1101:1179:2100 length=101 Is this okay? I am a first year graduate, thank you for your patience. |
4楼2015-01-19 13:40:24
wizardfan
至尊木虫 (著名写手)
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小木虫: 金币+0.5, 给个红包，谢谢回帖
小木虫: 金币+0.5, 给个红包，谢谢回帖
|
how sure you are that this is a pair-end data? Normally two files for pair-end data, named like ***_1.fastaq and ***_2.fastq. In ***_1.fastq, the headers of sequences are like ********/1, so as in the second file. There is a public server for you to use Trinity https://galaxy.cbio.mskcc.org/ |
5楼2015-01-20 10:18:19