Closed f0t1h closed 4 years ago
ydLiu-HIT
commented
4 years ago Hi， It is unbelievable, I check my code and couldn't found any error. What's more, I find that the length of the sequence and the qual strings are different. So hope you can check this read itself, or you can share the read and tell me your reference genome and your command lines which you get the result, I will look into it.
Good luck. Yadong
f0t1h
commented
4 years ago Read is as follows
@1947ec81-72ed-41df-91cd-01139e18d2f7 runid=a0233dab4f35e46d768c316fdf5bf0a86a67ee47 sampleid=Notts_Run4_20171030_DirectRNA_rs1 read=150 ch=383 start_time=2017-10-30T16:53:50Z
AAAUACUACCGUAUGGCCCACCAAUUACCCCAUACUCCUUAUUCCUCAUCACCCAACUAAAAAUAUUAACACACAAUCACCUACCUCCCUUCCAAAGCCAUAAAAAAUAAAAAUUAUCAUUACCUGAGAACCAAAUGGGAACGAAAAAUGUCAUCAUUCAUUGCCCUCAAUACCUAGGCCUACCGCCGCAGUACUGAUCAUUCAUUUCCCCUCUAUUGAUCCCCACCUCCAAUAUCUCAUCAACACUAUAAGUAAUCACCACCCAACAAUGUAAUCAAACUAACCUCAAAACAAUGAUAUAUACACAUUAAAGGACGAUAACCUGAUCUCUUAUACUAGUAUCCUUGCUAUUUUUAUUGCCUCCAACCCUCGGACUCCUGCCUCACUCAUUUACACCAUCACCCAACUAUUAUAAACCUAGCCAUGGCCAUACCCAACAUGAGCGGGCGCAGUGAUUAUAGGCUUUGGCUAAGAUUAAAUGUCCUAAUCCUACUUUUACCACAAGGCACACCUACACCCUAUCCCCCAUACUAGUAUCGAAAACCAUCAGCCAACCAUUCAUUCGUAGCCCUGGCGUACGCCUAACCGUUAUAACUGCAGGCCACCUACAUUGUCCUAAUUGGAAGUGCACCUAGCGGCAUCAACCAUUAACCUUCCCUCUACUUAUCAUCUUCAUCAAUUCUAAUUUGCUAUAUCCAAGAAAUCGCUGUGCCAAUCCAAGCCAUCUUUUACACUUUAGUAGCUCUACCUGCUCGGCAACACAUAAAU
+
37$555458?7/.,44=('(5/)79>4*D9927(*,)&%%&%%-/268637@<@@@169DB>?3/4<($$#%&+05+',*7:*'()0:</,7:;>>=333+6899>=4:<?=@<12,&)#$$('+.021457563).99<;=7%>=680/0%#&*-(%##$3,-3-*%%'%#).177<440)./(#'*-1374./82312*&$#)(.(7/3*&../+-3/)424&*.*,1..&$-%/.-''1../&))##"'1310##%%&++-/4431)+$%(($*;<0%$$&4$06:56661&0+7%,-323)((&%%=776I/0"#,56:9;B>&&'+6,752//49=:079<2%(--+/46261))'$($(#'%($.+6943/08,.($&'&036;0212/113570>;5/,-73-./;>@B<:<<300.-;<<67-(+,,(&&&&/)*3&1/0((',/2085**.634%-13*'(&*1;<11*$*'$0+%'$$+*%#()%-(#$&#$"$)&#%*%&552=(550.#)(,2132*0//+3/.**232333211-'0/-$$$/6//15''#"'1245(%1.'-45,52&#&%(,0$68+'&',)-*-)*-&.+(+$"$'&#%(#%%((',$#"&/)&$.1+-,'$),/)13355&;:960*(%1/#&'%'%%$5..,##%%$#$%)'%%-+*-%&##(&%*+,+$2676$6'#"%%%#&)*//%.&&&'##&"&&###$##$$$(0/+)*&+/32652'%&)$&(&&&)(')*')
Reference is GRCh38.97
ydLiu-HIT
commented
4 years ago Hi,
I have re-run you reads with the command (v1.5.5): deSALT aln GRCh38_index/ error.fa I got without any error:
1947ec81-72ed-41df-91cd-01139e18d2f7 0 chrM 8377 60 22M2D5M1D12M5D30M1I6M2D1M2D13M1D7M1D20M2D15M1D4M2I9M1D4M3D12M2D8M1I10M1D21M1D4M1D23M1D15M2I1M1D23M2D21M1D6M4D6M1D13M2I30M1D14M2D1M1D3M2D30M1D13M1D21M1I36M2D8M2D9M1I9M1D24M2D3M1I11M4D5M1I15M1D9M1D10M1D16M3D18M2D20M1D2M1D31M2D14M1I11M1D4M1D1M1D18M1D3M2D10M1D7M1D6M1D4M1D2M1D24M2S * 0 0 AAATACTACCGTATGGCCCACCAATTACCCCATACTCCTTATTCCTCATCACCCAACTAAAAATATTAACACACAATCACCTACCTCCCTTCCAAAGCCATAAAAAATAAAAATTATCATTACCTGAGAACCAAATGGGAACGAAAAATGTCATCATTCATTGCCCTCAATACCTAGGCCTACCGCCGCAGTACTGATCATTCATTTCCCCTCTATTGATCCCCACCTCCAATATCTCATCAACACTATAAGTAATCACCACCCAACAATGTAATCAAACTAACCTCAAAACAATGATATATACACATTAAAGGACGATAACCTGATCTCTTATACTAGTATCCTTGCTATTTTTATTGCCTCCAACCCTCGGACTCCTGCCTCACTCATTTACACCATCACCCAACTATTATAAACCTAGCCATGGCCATACCCAACATGAGCGGGCGCAGTGATTATAGGCTTTGGCTAAGATTAAATGTCCTAATCCTACTTTTACCACAAGGCACACCTACACCCTATCCCCCATACTAGTATCGAAAACCATCAGCCAACCATTCATTCGTAGCCCTGGCGTACGCCTAACCGTTATAACTGCAGGCCACCTACATTGTCCTAATTGGAAGTGCACCTAGCGGCATCAACCATTAACCTTCCCTCTACTTATCATCTTCATCAATTCTAATTTGCTATATCCAAGAAATCGCTGTGCCAATCCAAGCCATCTTTTACACTTTAGTAGCTCTACCTGCTCGGCAACACATAAAT 37$555458?7/.,44=('(5/)79>4*D9927(*,)&%%&%%-/268637@<@@@169DB>?3/4<($$#%&+05+',*7:*'()0:</,7:;>>=333+6899>=4:<?=@<12,&)#$$('+.021457563).99<;=7%>=680/0%#&*-(%##$3,-3-*%%'%#).177<440)./(#'*-1374./82312*&$#)(.(7/3*&../+-3/)424&*.*,1..&$-%/.-''1../&))##"'1310##%%&++-/4431)+$%(($*;<0%$$&4$06:56661&0+7%,-323)((&%%=776I/0"#,56:9;B>&&'+6,752//49=:079<2%(--+/46261))'$($(#'%($.+6943/08,.($&'&036;0212/113570>;5/,-73-./;>@B<:<<300.-;<<67-(+,,(&&&&/)*3&1/0((',/2085**.634%-13*'(&*1;<11*$*'$0+%'$$+*%#()%-(#$&#$"$)&#%*%&552=(550.#)(,2132*0//+3/.**232333211-'0/-$$$/6//15''#"'1245(%1.'-45,52&#&%(,0$68+'&',)-*-)*-&.+(+$"$'&#%(#%%((',$#"&/)&$.1+-,'$),/)13355&;:960*(%1/#&'%'%%$5..,##%%$#$%)'%%-+*-%&##(&%*+,+$2676$6'#"%%%#&)*//%.&&&'##&"&&###$##$$$(0/+)*&+/32652'%&)$&(&&&)(')*') NM:i:136 ms:i:407 AS:i:407 nn:i:0 XS:A:+Hope you can check your command and more details. Good luck. Yadong
For this read, deSALT-v1.5.5 doesn't put any tab between sequence and qual strings.